Methods and compositions for integration of an exogenous sequence within the genome of plants

ABSTRACT

Disclosed herein are methods and compositions for parallel or sequential transgene stacking in plants to produce plants with selected phenotypes.

CROSS-REFERENCE TO RELATED APPLICATIONS

The application claims the benefit of U.S. Provisional Application No.61/809,097, filed on Apr. 5, 2013 and U.S. Provisional Application No.61/820,461, filed on May 7, 2013, the disclosures of which are herebyincorporated by reference in their entireties herein.

STATEMENT OF RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSOREDRESEARCH

Not applicable.

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY

The official copy of the sequence listing is submitted electronicallyvia EFS-Web as an ASCII formatted sequence listing concurrently with thespecification. The sequence listing contained in this ASCII formatteddocument is part of the specification and is herein incorporated byreference in its entirety.

TECHNICAL FIELD

The present disclosure is in the field of genomic engineering,particularly in the integration of exogenous sequences into plants,including simultaneous genomic editing of multiple alleles over multiplegenomes, including in polyploid plants.

BACKGROUND

To meet the challenge of increasing global demand for food production,many effective approaches to improving agricultural productivity (e.g.,enhanced yield or engineered pest resistance) rely on either mutationbreeding or introduction of novel genes into the genomes of crop speciesby transformation. Both processes are inherently non-specific andrelatively inefficient. For example, conventional plant transformationmethods deliver exogenous DNA that integrates into the genome at randomlocations. The random nature of these methods makes it necessary togenerate and screen hundreds of unique random-integration events perconstruct in order to identify and isolate transgenic lines withdesirable attributes. Moreover, conventional transformation methodscreate several challenges for transgene evaluation including: (a)difficulty for predicting whether pleiotropic effects due to unintendedgenome disruption have occurred; and (b) difficulty for comparing theimpact of different regulatory elements and transgene designs within asingle transgene candidate, because such comparisons are complicated byrandom integration into the genome. As a result, conventional planttrait engineering is a laborious and cost intensive process with a lowprobability of success.

Precision gene modification overcomes the logistical challenges ofconventional practices in plant systems, and as such has been alongstanding but elusive goal in both basic plant biology research andagricultural biotechnology. However, with the exception of “genetargeting” via positive-negative drug selection in rice or the use ofpre-engineered restriction sites, targeted genome modification in allplant species, both model and crop, has until recently proven verydifficult. Terada et al. (2002) Nat Biotechnol 20(10):1030; Terada etal. (2007) Plant Physiol 144(2):846; D'Halluin et al. (2008) PlantBiotechnology J. 6(1):93.

Recently, methods and compositions for targeted cleavage of genomic DNAhave been described. Such targeted cleavage events can be used, forexample, to induce targeted mutagenesis, induce targeted deletions ofcellular DNA sequences, and facilitate targeted recombination andintegration at a predetermined chromosomal locus. See, for example,Urnov et al. (2010) Nature 435(7042):646-51; U.S. Pat. Nos. 8,586,526;8,586,363; 8,409,861; 8,106,255; 7,888,121; 8,409,861 and U.S. PatentPublications 20030232410; 20050026157; 20090263900; 20090117617;20100047805; 20100257638; 20110207221; 20110239315; 20110145940, thedisclosures of which are incorporated by reference in their entiretiesfor all purposes. Cleavage can occur through the use of specificnucleases such as engineered zinc finger nucleases (ZFN),transcription-activator like effector nucleases (TALENs), or using theCRISPR/Cas system with an engineered crRNA/tracr RNA (‘single guideRNA’) to guide specific cleavage. U.S. Patent Publication No.20080182332 describes the use of non-canonical zinc finger nucleases(ZFNs) for targeted modification of plant genomes; U.S. Pat. No.8,399,218 describes ZFN-mediated targeted modification of a plant EPSPSlocus; U.S. Pat. No. 8,329,986 describes targeted modification of aplant Zp15 locus and U.S. Pat. No. 8,592,645 describes targetedmodification of plant genes involved in fatty acid biosynthesis. Inaddition, Moehle et al. (2007) Proc. Natl. Acad, Sci. USA104(9):3055-3060 describes using designed ZFNs for targeted geneaddition at a specified locus. U.S. Patent Publication 20110041195describes methods of making homozygous diploid organisms.

Transgene (or trait) stacking has great potential for production ofplants, but has proven difficult. See, e.g., Halpin (2005) PlantBiotechnology Journal 3:141-155. In addition, polyploidy, where theorganism has two or more duplicated (autoploidy) or related (alloploid)paired sets of chromosomes, occurs more often in plant species than inanimals. For example, wheat has lines that are diploid (two sets ofchromosomes), tetraploid (four sets of chromosomes) and hexaploid (sixsets of chromosomes). In addition, many agriculturally important plantsof the genus Brassica are also allotetraploids.

Thus, there remains a need for compositions and methods for theidentification, selection and rapid advancement of stable targetedintegration into precise locations within a plant genome, includingsimultaneous modification of multiple alleles across different genomesof polyploid plants, for establishing stable, heritable geneticmodifications in a plant and its progeny.

SUMMARY

The present disclosure provides methods and compositions for precisiontransformation, gene targeting, targeted genomic modification andprotein expression in plants. In particular, the present disclosuredescribes a novel, transgenic marker-free strategy for integrating anexogenous sequence and to stack traits that exploit differentialselection at an endogenous locus (e.g., the acetohydroxyacid synthase(AHAS) locus) in plant genomes. The strategy facilitates generation ofplants that have one or more transgenes (or one or more genes ofinterest (GOI), wherein the transgenes do not include transgenicselectable marker genes) precisely positioned at an endogenous plantlocus, for example, at one or more AHAS paralogs. The methods andcompositions described herein enable both parallel and sequentialtransgene stacking in plant genomes at precisely the same genomiclocation, including simultaneous editing of multiple alleles acrossmultiple genomes of polyploid plant species. In addition, the methodsand compositions of the invention allow for exogenous transgenicselectable marker-free selection and/or genomic modification of anendogenous gene in which the genomic modification produces a mutation inthe endogenous gene such that the endogenous gene produces a productthat results in an herbicide tolerant plant (e.g., by virtue ofexploiting known mutations in an endogenous gene such as known mutationsin AHAS gene that confer tolerance to Group B herbicides, or ALSinhibitor herbicides such as imidazolinone or sulfonylurea). Alsoprovided are cells (e.g., seeds), cell lines, organisms (e.g., plants),etc. comprising these transgene-stacked and/or simultaneously-modifiedalleles. The targeted genomic editing (insertions, deletions, mutations,transgene stacking) can result, for example, in increased crop yield, aprotein encoding disease resistance, a protein that increases growth, aprotein encoding insect resistance, a protein encoding herbicidetolerance and the like. Increased yield can include, for example,increased amount of fruit or grain yield, increased biomass of the plant(or fruit or grain of the plant), higher content of fruit flesh, largerplants, increased dry weight, increased solids context, higher totalweight at harvest, enhanced intensity and/or uniformity of color of thecrop, altered chemical (e.g., oil, fatty acid, carbohydrate, protein)characteristics, etc.

Thus, in one aspect, disclosed herein are methods and compositions forprecise, genomic modification (e.g., transgene stacking) at one or moreendogenous alleles of a plant gene. In certain embodiments, thetransgene(s) is(are) integrated into an endogenous locus of a plantgenome (e.g., polyploid plant). Transgene integration includesintegration of multiple transgenes, which may be in parallel(simultaneous integration of one or more transgenes into one or morealleles) or sequential. In certain embodiments, the transgene does notinclude a transgenic marker, but is integrated into an endogenous locusthat is modified upon integration of the transgene comprising a trait,for example, integration of the transgene(s) into an endogenousacetohydroxyacid synthase (AHAS) locus (e.g., the 3′ untranslated regionof the AHAS locus) such that the transgene is expressed and the AHASlocus is modified to alter herbicide tolerance (e.g., Group Bherbicides, or ALS inhibitor herbicides such as imidazolinone orsulfonylurea). The transgene(s) is(are) integrated in a targeted mannerusing one or more non-naturally occurring nucleases, for example zincfinger nucleases, meganucleases, TALENs and/or a CRISPR/Cas system withan engineered single guide RNA. The transgene can comprise one or morecoding sequences (e.g., proteins), non-coding sequences and/or mayproduce one or more RNA molecules (e.g., mRNA, RNAi, siRNA, shRNA,etc.). In certain embodiments, the transgene integration is simultaneous(parallel). In other embodiments, sequential integration of one or moretransgenes (GOIs) is achieved, for example by the AHAS locus, byalternating between different herbicide (Group B, or ALS inhibitorherbicides such as imidazolinone or sulfonylurea) chemical selectionagents and known AHAS mutations conferring tolerance to those specificherbicides. Furthermore, any of the plant cells described herein mayfurther comprise one or more additional transgenes, in which theadditional transgenes are integrated into the genome at a differentlocus (or different loci) than the target allele(s) for transgenestacking. Thus, a plurality of endogenous loci may include integratedtransgenes in the cells described herein.

In another aspect, disclosed herein are polyploid plant cells in whichmultiple alleles of one or more genes across the different genomes(sub-genomes) have been simultaneously modified. The targetedmodifications may enhance or reduce gene activity (e.g., endogenous geneactivity and/or activity of an integrated transgene) in the polyploidplant, for example mutations in AHAS that alter (e.g., increase)herbicide tolerance.

In certain embodiments, the targeted genomic modification in thepolyploid plant cell comprises a small insertion and/or deletion, alsoknown as an indel. Any of the plant cells described herein may be withina plant or plant part (e.g., seeds, flower, fruit), for example, anyvariety of: wheat, soy, maize, potato, alfalfa, rice, barley, sunflower,tomato, Arabidopsis, cotton, Brassica species (including but not limitedto B. napus, B. rapa, B. oleracea, B. nigra, B. juncea, B. carinata),Brachypodium, timothy grass and the like.

In another aspect, described herein is a DNA-binding domain (e.g., zincfinger protein (ZFP)) that specifically binds to a gene involved inherbicide tolerance, for example, an AHAS gene. The zinc finger proteincan comprise one or more zinc fingers (e.g., 2, 3, 4, 5, 6, 7, 8, 9 ormore zinc fingers), and can be engineered to bind to any sequence withina polyploid plant genome. Any of the zinc finger proteins describedherein may bind to a target site within the coding sequence of thetarget gene or within adjacent sequences (e.g., promoter or otherexpression elements). In certain embodiments, the zinc finger proteinbinds to a target site in an AHAS gene, for example, as shown in Table 3and Table 13. The recognition helix regions of exemplary AHAS-bindingzinc fingers are shown in Table 2 and Table 12. One or more of thecomponent zinc finger binding domains of the zinc finger protein can bea canonical (C2H2) zinc finger or a non-canonical (e.g., C3H) zincfinger (e.g., the N-terminal and/or C-terminal zinc finger can be anon-canonical finger).

In another aspect, disclosed herein are fusion proteins, each fusionprotein comprising a DNA-binding domain (e.g., a zinc finger protein)that specifically binds to multiple alleles of a gene in polyploid plantgenomes. In certain embodiments, the proteins are fusion proteinscomprising a zinc finger protein and a functional domain, for example atranscriptional activation domain, a transcriptional repression domainand/or a cleavage domain (or cleavage half-domain). In certainembodiments, the fusion protein is a zinc finger nuclease (ZFN).Cleavage domains and cleavage half domains can be obtained, for example,from various restriction endonucleases and/or homing endonucleases. Inone embodiment, the cleavage half-domains are derived from a Type IISrestriction endonuclease (e.g., Fok I).

In other aspects, provided herein are polynucleotides encoding any ofthe DNA-binding domains and/or fusion proteins described herein. Incertain embodiments, described herein is an expression vector comprisinga polynucleotide, encoding one or more DNA-binding domains and/or fusionproteins described herein, operably linked to a promoter. In oneembodiment, one or more of the fusion proteins are ZFNs.

The DNA-binding domains and fusion proteins comprising these DNA-bindingdomains bind to and/or cleave two or more endogenous genes in apolyploid genome (e.g., an AHAS gene) within the coding region of thegene or in a non-coding sequence within or adjacent to the gene, suchas, for example, a leader sequence, trailer sequence or intron, orpromoter sequence, or within a non-transcribed region, either upstreamor downstream of the coding region, for example the 3′ untranslatedregion. In certain embodiments, the DNA-binding domains and/or fusionproteins bind to and/or cleave a coding sequence or a regulatorysequence of the target gene.

In another aspect, described herein are compositions comprising one ormore proteins, fusion proteins or polynucleotides as described herein.Polyploid plant cells contain multiple genomic allelic targets. Thus,compositions described herein may comprise one or more DNA-bindingproteins (and polynucleotides encoding same) that target (andsimultaneously modify) multiple alleles present in multiple genomes(also referred to as sub-genomes) of a polyploid plant cell. TheDNA-binding proteins may target all genes (paralogs), one or multiple(but less than all) selected alleles.

In another aspect, provided herein is a method for simultaneouslyaltering multiple alleles across the multiple genomes of a polyploidplant cell, the method comprising, expressing one or more DNA-bindingdomain proteins (e.g., zinc finger proteins such as zinc fingernucleases) in the cell such that multiple alleles of the polyploid plantare altered. In certain embodiments, altering expression of one or moreAHAS genes in a plant cell, the method comprising, expressing one ormore DNA-binding domain containing proteins (e.g., zinc finger proteins)in the cell such that expression of AHAS is altered. In certainembodiments, the methods comprise using a pair of zinc finger nucleasesto create a small insertion and/or deletion (“indel”) that disruptsendogenous gene expression. In other embodiments, the methods compriseusing a pair of zinc finger nucleases to enhance gene expression, forexample via targeted insertion of an exogenous sequence (e.g., donorsequence, GOI, or transgene) or expression enhancing element. Thealtered gene expression/function can result in increased photosynthesis,increased herbicide tolerance and/or modifications in growth withinplant cells.

In another aspect, provided herein are nucleic acids and antibodies, andmethods of using the same, for detecting and/or measuring alteredexpression of and modifications to multiples alleles of a gene (e.g.,AHAS).

In another aspect, described herein is a method for simultaneouslymodifying one or more endogenous genes in a polyploid plant cell. Incertain embodiments, the method comprising: (a) introducing, into thepolyploid plant cell, one or more expression vectors encoding one ormore nucleases (e.g., ZFNs, TALENs, meganucleases and/or CRISPR/Cassystems) that bind to a target site in the one or more genes underconditions such that the nucleases cleave the one or more endogenousgenes, thereby modifying the one or more endogenous (e.g., AHAS) genes.In other embodiments, more than one allele of an endogenous gene iscleaved, for example in polyploid plants. In other embodiments, one ormore alleles of more than one endogenous gene is cleaved. Furthermore,in any of the methods described herein, cleavage of the one or moregenes may result in deletion, addition and/or substitution ofnucleotides in the cleaved region, for example such that AHAS activityis altered (e.g., enhanced or reduced), thereby allowing for assessmentof, for example, transgene integration at or near the modifiedendogenous genes.

In yet another aspect, described herein is a method for introducing oneor more exogenous sequences into the genome of a plant cell, the methodcomprising the steps of: (a) contacting the cell with the one or moreexogenous sequences (e.g., donor vector, transgene or GOI, orcombinations thereof); and (b) expressing one or more nucleases (e.g.,ZFNs, TALENs, meganucleases and/or CRISPR/Cas systems) as describedherein in the cell, wherein the one or more nucleases cleave chromosomalDNA; such that cleavage of chromosomal DNA in step (b) stimulatesincorporation of the exogenous sequence into the genome by homologousrecombination. In certain embodiments, the chromsomal DNA is modifiedsuch that the chromosomal sequence (e.g., endogenous gene) is mutated toexpresses a product that produces a selectable phenotype (e.g.,herbicide tolerance). Multiple exogenous sequences may be integratedsimultaneously (in parallel) or the steps may be repeated for sequentialaddition of transgenes (transgene stacking). In certain embodiments, theone or more transgenes are introduced within an AHAS gene, for examplethe 3′ untranslated region. In any of the methods described herein, theone or more nucleases may be fusions between a nuclease (cleavage)domain (e.g., a cleavage domain of a Type IIs restriction endonucleaseor a meganuclease) and an engineered zinc finger binding domain. Inother embodiments, the nuclease comprises a TAL effector domain, ahoming endonuclease and/or a Crispr/Cas single guide RNA. In any of themethods described herein, the exogenous sequence may encode a proteinproduct and/or produce an RNA molecule. In any of the methods describedherein, the exogenous sequence may be integrated such that endogenouslocus into which the exogenous sequence(s) is(are) inserted is modifiedto produce one or more measurable phenotypes or markers (e.g., herbicidetolerance by mutation of endogenous AHAS).

In yet another aspect, disclosed herein is a plant cell comprising atargeted genomic modification to one or more alleles of an endogenousgene in the plant cell, wherein the genomic modification followscleavage by a site specific nuclease, and wherein the genomicmodification produces a mutation in the endogenous gene such that theendogenous gene produces a product that results in an herbicide tolerantplant cell. In an embodiment, the genomic modification comprisesintegration of one or more exogenous sequences. In a further embodiment,the genomic modification comprises introduction of one or more indelsthat mutate the endogenous gene. In an additional embodiment, theendogenous gene with the genomic modification encodes a protein thatconfers tolerance to sulfonylurea herbicides. In an embodiment, theendogenous gene with the genomic modification encodes a protein thatconfers tolerance to imidazolinone herbicides. In a further embodiment,the exogenous sequence does not encode a transgenic selectable marker.In an additional embodiment, the exogenous sequence encodes a proteinselected from the group consisting of a protein that increases cropyield, a protein encoding disease resistance, a protein that increasesgrowth, a protein encoding insect resistance, a protein encodingherbicide tolerance, and combinations thereof. In subsequentembodiments, the increased crop yield comprises an increase in fruityield, grain yield, biomass, fruit flesh content, size, dry weight,solids content, weight, color intensity, color uniformity, alteredchemical characteristics, or combinations thereof. In certainembodiments, the endogenous gene is an endogenous acetohydroxyacidsynthase (AHAS) gene. In additional embodiments, the two or moreexogenous sequences are integrated into the endogenous gene. In afurther aspect, the plant cell is a polyploid plant cell. In anembodiment, the site specific nuclease comprises a zinc fingerDNA-binding domain, and a FokI cleavage domain. In yet anotherembodiment, the zinc finger DNA-binding domain encodes a protein thatbinds to a target site selected from the group consisting of SEQ IDNOs:35-56 and 263-278. In a further embodiment, the plant is selectedfrom the group consisting of wheat, soy, maize, potato, alfalfa, rice,barley, sunflower, tomato, Arabidopsis, cotton, Brassica species, andtimothy grass.

In yet another aspect, disclosed herein is a plant, plant part, seed, orfruit comprising one or more plant cells comprising a targeted genomicmodification to one or more alleles of an endogenous gene in the plantcell, wherein the genomic modification follows cleavage by a sitespecific nuclease, and wherein the genomic modification produces amutation in the endogenous gene such that the endogenous gene produces aproduct that results in an herbicide tolerant plant cell.

In yet another aspect, disclosed herein is a method for making a plantcell as disclosed herein above, the method comprising: expressing one ormore site specific nucleases in the plant cell; and, modifying one ormore alleles of an endogenous gene across multiple genomes of apolyploid plant cell. In an embodiment, the endogenous gene is anacetohydroxyacid synthase (AHAS) gene. In a further embodiment, themodification disrupts expression of the endogenous gene. In yet anotherembodiment, the modification comprises integration of one or moreexogenous sequences into one or more alleles of the endogenous gene.Furthermore, a plant, plant part, seed, or fruit comprising one or moreplant cells produced by the method are disclosed herein as an aspect ofthe disclosure.

In yet another aspect, disclosed herein is a zinc finger protein thatbinds to a target site selected from the group consisting of SEQ IDNOs:35-56 and 263-278. In a further embodiment, the zinc finger proteinscomprise the recognition helix regions shown in a single row of Table 2or Table 12.

In yet another aspect, described herein is a method of integrating oneor more exogenous sequences into the genome of a plant cell, the methodcomprising: expressing one or more site specific nucleases in the plantcell, wherein the one or more nucleases target and cleave chromosomalDNA of one or more endogenous loci; integrating one or more exogenoussequences into the one or more endogenous loci within the genome of theplant cell, wherein the one or more endogenous loci are modified suchthat the endogenous gene is mutated to expresses a product that resultsin a selectable phenotype in the plant cell; and, selecting plant cellsthat express the selectable phenotype, wherein plant cells are selectedwhich incorporate the one or more exogenous sequences. In a furtherembodiment, the one or more exogenous sequences are selected from thegroup consisting of a donor polynucleotide, a transgene, or anycombination thereof. In a subsequent embodiment, the integration of theone or more exogenous sequences occurs by homologous recombination ornon-homologous end joining. In an additional embodiment, the one or moreexogenous sequences are incorporated simultaneously or sequentially intothe one or more endogenous loci. In further embodiments, the one or moreendogenous loci comprise an acetohydroxyacid synthase (AHAS) gene. In anembodiment, the AHAS gene is located on an A, B, or D genome of apolyploidy genome. In another embodiment, the one or more exogenoussequences are integrated into the AHAS gene. In yet another embodiment,the one or more exogenous sequences encode a S653N AHAS mutation. In anadditional embodiment, the one or more exogenous sequences encode aP197S AHAS mutation. In a subsequent embodiment, the site specificnuclease is selected from the group consisting of a zinc fingernuclease, a TAL effector domain nuclease, a homing endonuclease, and aCrispr/Cas single guide RNA nuclease. In a further embodiment, the sitespecific nuclease comprises a zinc finger DNA-binding domain, and a FokIcleavage domain. In an embodiment, the one or more exogenous sequencesencode a transgene or produce an RNA molecule. In a subsequentembodiment, the transgene encodes a protein selected from the groupconsisting of a protein that increases crop yield, a protein encodingdisease resistance, a protein that increases growth, a protein encodinginsect resistance, a protein encoding herbicide tolerance, andcombinations thereof. In further embodiments, the integration of thetransgene further comprises introduction of one or more indels thatdisrupt expression of the one or more endogenous loci and produce theselectable phenotype. Subsequent embodiments of the method furthercomprise the steps of; culturing the selected plant cells comprising theone or more exogenous sequences; and, obtaining a whole plant comprisingthe one or more exogenous sequences integrated within the one or moreendogenous loci of the plant genome. In an additional embodiment, aselection agent comprising an imidazolinone, or a sulfonylurea selectionagent is used to select the plant cells. In other embodiments, the wholeplant comprising the one or more exogenous sequences integrated withinthe one or more endogenous loci of the plant genome is further modifiedto incorporate an additional exogenous sequence within the endogenousloci of the plant genome. In further embodiments, the one or moreexogenous sequences do not encode a transgenic selectable marker.

In a still further aspect, a plant cell obtained according to any of themethods described herein is also provided.

In another aspect, provided herein is a plant comprising a plant cell asdescribed herein.

In another aspect, provided herein is a seed from a plant comprising theplant cell that is obtained as described herein.

In another aspect, provided herein is fruit obtained from a plantcomprising plant cell obtained as described herein.

In any of the compositions (cells or plants) or methods describedherein, the plant cell can comprise a monocotyledonous or dicotyledonousplant cell. In certain embodiments, the plant cell is a crop plant, forexample, wheat, tomato (or other fruit crop), potato, maize, soy,alfalfa, etc.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a plasmid map of pDAB109350.

FIG. 2 is a plasmid map of pDAB109360.

FIG. 3 is a plasmid map of pDAS000132.

FIG. 4 is a plasmid map of pDAS000133.

FIG. 5 is a plasmid map of pDAS000134.

FIG. 6 is a plasmid map of pDAS000135.

FIG. 7 is a plasmid map of pDAS000131.

FIG. 8 is a plasmid map of pDAS000153.

FIG. 9 is a plasmid map of pDAS000150.

FIG. 10 is a plasmid map of pDAS000143.

FIG. 11 is a plasmid map of pDAS000164.

FIG. 12 is a plasmid map of pDAS000433.

FIG. 13 is a plasmid map of pDAS000434.

FIG. 14, panels A and B, are schematics depicting exogenous marker-free,sequential transgene stacking at an endogenous AHAS locus in the wheatgenome of Triticum aestivum using ZFN-mediated, NHEJ-directed DNArepair. FIG. 14A depicts a first transgene stack; FIG. 14B depicts asecond transgene stack.

FIG. 15, panels A and B, are schematics depicting exogenous marker-free,sequential transgene stacking at an endogenous AHAS locus in the wheatgenome of Triticum aestivum using ZFN-mediated, HDR-directed DNA repair.FIG. 15A depicts a first transgene stack; FIG. 15B depicts a secondtransgene stack.

FIG. 16 is a schematic showing a linear map of pDAS000435.

FIG. 17 is a schematic showing a linear map of pDAS000436.

FIG. 18 is a plasmid map of pDAS0000004.

FIG. 19 is a plasmid map of QA_pDAS000434.

DETAILED DESCRIPTION

The present disclosure relates to methods and compositions for exogenoussequence integration, including parallel (simultaneous) or sequentialexogenous sequence integration (including transgene stacking) in a plantspecies, including in a polyploid plant. The methods and compositionsdescribed herein are advantageous in providing targeted integration intoa selected locus without the use of an exogenous transgenic marker toassess integration. In particular, differential selection at anendogenous locus, with a transgenic marker-free donor design, has beendemonstrated to bias selection for targeted transgenic events byreducing the number of illegitimate integrated events recovered (Shuklaet al. (2009) Nature 459(7245):437-41). In addition, the disclosurerelates to genomic modification (e.g., mutation) of an endogenous locus,which mutation can result in production of a product that serves as amarker (phenotype). Thus, the present disclosure provides for exogenoussequence integration, including transgene stacking, into an endogenouslocus, which endogenous locus can serve as a marker for integration(e.g., the AHAS locus in which single mutations can impart herbicidetolerance).

Integration of the exogenous sequence(s) (e.g., into the AHAS locus) isfacilitated by targeted double-strand cleavage of endogenous sequence,for example by cleavage of a sequence located in the 3′ untranslatedregion. Cleavage is targeted to this region through the use of fusionproteins comprising a DNA-binding domain, such as a meganucleaseDNA-binding domain, a leucine zipper DNA-binding domain, a TALDNA-binding domain, a zinc finger protein (ZFP); or through the use of aCrispr/Cas RNA or chimeric combinations of the aforementioned. Suchcleavage stimulates integration of the donor nucleic acid sequence(s)at, or near the endogenous cleavage site. Integration of exogenoussequences can proceed through both homology-dependent andhomology-independent mechanisms, and the selection of precisely targetedevents is achieved through screening for a selectable marker (e.g.,tolerance to a specific Group B herbicide, or ALS inhibitor herbicidessuch as imidazolinone or sulfonylurea) which is only functional incorrectly targeted events.

In certain embodiments, the nuclease(s) comprise one or more ZFNs, oneor more TALENs, one or more meganucleases and/or one or more CRISPR/Casnuclease systems. ZFNs and TALENs typically comprise a cleavage domain(or a cleavage half-domain) and a zinc finger DNA binding orTALE-effector DNA binding domain and may be introduced as proteins, aspolynucleotides encoding these proteins or as combinations ofpolypeptides and polypeptide-encoding polynucleotides. ZFNs and TALENscan function as dimeric proteins following dimerization of the cleavagehalf-domains. Obligate heterodimeric nucleases, in which the nucleasemonomers bind to the “left” and “right” recognition domains canassociate to form an active nuclease have been described. See, e.g.,U.S. Pat. Nos. 8,623,618; 7,914,796; 8034,598. Thus, given theappropriate target sites, a “left” monomer could form an active nucleasewith any “right” monomer. This significantly increases the number ofuseful nuclease sites based on proven left and right domains that can beused in various combinations. For example, recombining the binding sitesof four homodimeric nucleases yields an additional twelve heterodimericnucleases. More importantly, it enables a systematic approach totransgenic design such that every new introduced sequence becomesflanked with a unique nuclease binding site that can be used to excisethe gene back out or to target additional genes next to it.Additionally, this method can simplify strategies of stacking into asingle locus that is driven by nuclease-dependent double-strand breaks.

A zinc finger binding domain can be a canonical (C2H2) zinc finger or anon-canonical (e.g., C3H) zinc finger. See, e.g., U.S. PatentPublication No. 20080182332. Furthermore, the zinc finger binding domaincan comprise one or more zinc fingers (e.g., 2, 3, 4, 5, 6, 7, 8, 9 ormore zinc fingers), and can be engineered to bind to any sequence withinany endogenous gene, for example an AHAS gene. The presence of such afusion protein (or proteins) in a cell results in binding of the fusionprotein(s) to its (their) binding site(s) and cleavage within the targetgene(s).

General

Practice of the methods, as well as preparation and use of thecompositions disclosed herein employ, unless otherwise indicated,conventional techniques in molecular biology, biochemistry, chromatinstructure and analysis, computational chemistry, cell culture,recombinant DNA and related fields as are within the skill of the art.These techniques are fully explained in the literature. See, forexample, Sambrook et al. MOLECULAR CLONING: A LABORATORY MANUAL, Secondedition, Cold Spring Harbor Laboratory Press, 1989 and Third edition,2001; Ausubel et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley& Sons, New York, 1987 and periodic updates; the series METHODS INENZYMOLOGY, Academic Press, San Diego; Wolffe, CHROMATIN STRUCTURE ANDFUNCTION, Third edition, Academic Press, San Diego, 1998; METHODS INENZYMOLOGY, Vol. 304, “Chromatin” (P. M. Wassarman and A. P. Wolffe,eds.), Academic Press, San Diego, 1999; and METHODS IN MOLECULARBIOLOGY, Vol. 119, “Chromatin Protocols” (P. B. Becker, ed.) HumanaPress, Totowa, 1999.

DEFINITIONS

The terms “nucleic acid,” “polynucleotide,” and “oligonucleotide” areused interchangeably and refer to a deoxyribonucleotide orribonucleotide polymer, in linear or circular conformation, and ineither single- or double-stranded form. For the purposes of the presentdisclosure, these terms are not to be construed as limiting with respectto the length of a polymer. The terms can encompass known analogues ofnatural nucleotides, as well as nucleotides that are modified in thebase, sugar and/or phosphate moieties (e.g., phosphorothioatebackbones). In general, an analogue of a particular nucleotide has thesame base-pairing specificity; i.e., an analogue of A will base-pairwith T.

The terms “polypeptide,” “peptide” and “protein” are usedinterchangeably to refer to a polymer of amino acid residues. The termalso applies to amino acid polymers in which one or more amino acids arechemical analogues or modified derivatives of correspondingnaturally-occurring amino acids.

“Binding” refers to a sequence-specific, non-covalent interactionbetween macromolecules (e.g., between a protein and a nucleic acid). Notall components of a binding interaction need be sequence-specific (e.g.,contacts with phosphate residues in a DNA backbone), as long as theinteraction as a whole is sequence-specific. Such interactions aregenerally characterized by a dissociation constant (K_(d)) of 10⁻⁶ M⁻¹or lower. “Affinity” refers to the strength of binding: increasedbinding affinity being correlated with a lower K_(d).

A “binding protein” is a protein that is able to bind to anothermolecule. A binding protein can bind to, for example, a DNA molecule (aDNA-binding protein), an RNA molecule (an RNA-binding protein) and/or aprotein molecule (a protein-binding protein). In the case of aprotein-binding protein, it can bind to itself (to form homodimers,homotrimers, etc.) and/or it can bind to one or more molecules of adifferent protein or proteins. A binding protein can have more than onetype of binding activity. For example, zinc finger proteins haveDNA-binding, RNA-binding and protein-binding activity.

A “zinc finger DNA binding protein” (or binding domain) is a protein, ora domain within a larger protein, that binds DNA in a sequence-specificmanner through one or more zinc fingers, which are regions of amino acidsequence within the binding domain whose structure is stabilized throughcoordination of a zinc ion. The term zinc finger DNA binding protein isoften abbreviated as zinc finger protein or ZFP.

A “TALE DNA binding domain” or “TALE” is a polypeptide comprising one ormore TALE repeat domains/units. The repeat domains are involved inbinding of the TALE to its cognate target DNA sequence. A single “repeatunit” (also referred to as a “repeat”) is typically 33-35 amino acidsand includes hypervariable diresidues at positions 12 and/or 13 referredto as the Repeat Variable Diresidue (RVD) involved in DNA-bindingspecificity. TALE repeats exhibit at least some sequence homology withother TALE repeat sequences within a naturally occurring TALE protein.See, e.g., U.S. Pat. No. 8,586,526.

Zinc finger binding and TALE domains can be “engineered” to bind to apredetermined nucleotide sequence. Non-limiting examples of methods forengineering zinc finger proteins are design and selection. A designedzinc finger protein is a protein not occurring in nature whosedesign/composition results principally from rational criteria. Rationalcriteria for design include application of substitution rules andcomputerized algorithms for processing information in a database storinginformation of existing ZFP designs and binding data. See, for example,U.S. Pat. Nos. 6,140,081; 6,453,242; and 6,534,261; see also WO98/53058; WO 98/53059; WO 98/53060; WO 02/016536 and WO 03/016496.

A “selected” zinc finger protein or TALE is a protein not found innature whose production results primarily from an empirical process suchas phage display, interaction trap or hybrid selection. See e.g., U.S.Pat. No. 8,586,526, U.S. Pat. No. 5,789,538; U.S. Pat. No. 5,925,523;U.S. Pat. No. 6,007,988; U.S. Pat. No. 6,013,453; U.S. Pat. No.6,200,759; WO 95/19431; WO 96/06166; WO 98/53057; WO 98/54311; WO00/27878; WO 01/60970 WO 01/88197 and WO 02/099084.

The term “sequence” refers to a nucleotide sequence of any length, whichcan be DNA or RNA; can be linear, circular or branched and can be eithersingle-stranded or double stranded. The term “donor sequence” refers toa nucleotide sequence that is inserted into a genome. A donor sequencecan be of any length, for example between 2 and 10,000 nucleotides inlength (or any integer value therebetween or thereabove), preferablybetween about 100 and 1,000 nucleotides in length (or any integertherebetween), more preferably between about 200 and 500 nucleotides inlength.

A “homologous, non-identical sequence” refers to a first sequence whichshares a degree of sequence identity with a second sequence, but whosesequence is not identical to that of the second sequence. For example, apolynucleotide comprising the wild-type sequence of a mutant gene ishomologous and non-identical to the sequence of the mutant gene. Incertain embodiments, the degree of homology between the two sequences issufficient to allow homologous recombination therebetween, utilizingnormal cellular mechanisms. Two homologous non-identical sequences canbe any length and their degree of non-homology can be as small as asingle nucleotide (e.g., for correction of a genomic point mutation bytargeted homologous recombination) or as large as 10 or more kilobases(e.g., for insertion of a gene at a predetermined ectopic site in achromosome). Two polynucleotides comprising the homologous non-identicalsequences need not be the same length. For example, an exogenouspolynucleotide (i.e., donor polynucleotide) of between 20 and 10,000nucleotides or nucleotide pairs can be used.

Techniques for determining nucleic acid and amino acid sequence identityare known in the art. Typically, such techniques include determining thenucleotide sequence of the mRNA for a gene and/or determining the aminoacid sequence encoded thereby, and comparing these sequences to a secondnucleotide or amino acid sequence. Genomic sequences can also bedetermined and compared in this fashion. In general, identity refers toan exact nucleotide-to-nucleotide or amino acid-to-amino acidcorrespondence of two polynucleotides or polypeptide sequences,respectively. Two or more sequences (polynucleotide or amino acid) canbe compared by determining their percent identity. The percent identityof two sequences, whether nucleic acid or amino acid sequences, is thenumber of exact matches between two aligned sequences divided by thelength of the shorter sequences and multiplied by 100. An approximatealignment for nucleic acid sequences is provided by the local homologyalgorithm of Smith and Waterman, Advances in Applied Mathematics2:482-489 (1981). This algorithm can be applied to amino acid sequencesby using the scoring matrix developed by Dayhoff, Atlas of ProteinSequences and Structure, M. O. Dayhoff ed., 5 suppl. 3:353-358, NationalBiomedical Research Foundation, Washington, D.C., USA, and normalized byGribskov, Nucl. Acids Res. 14(6):6745-6763 (1986). An exemplaryimplementation of this algorithm to determine percent identity of asequence is provided by the Genetics Computer Group (Madison, Wis.) inthe “BestFit” utility application. Suitable programs for calculating thepercent identity or similarity between sequences are generally known inthe art, for example, another alignment program is BLAST, used withdefault parameters. For example, BLASTN and BLASTP can be used using thefollowing default parameters: genetic code=standard; filter=none;strand=both; cutoff=60; expect=10; Matrix=BLOSUM62 (for BLASTP);Descriptions=50 sequences; sort by=HIGH SCORE; Databases=non-redundant,GenBank+EMBL+DDBJ+PDB+GenBank CDS translations+Swissprotein+Spupdate+PIR. Details of these programs can be found on theinternet. With respect to sequences described herein, the range ofdesired degrees of sequence identity is approximately 80% to 100% andany integer value therebetween. Typically the percent identities betweensequences are at least 70-75%, preferably 80-82%, more preferably85-90%, even more preferably 92%, still more preferably 95%, and mostpreferably 98% sequence identity.

Alternatively, the degree of sequence similarity between polynucleotidescan be determined by hybridization of polynucleotides under conditionsthat allow formation of stable duplexes between homologous regions,followed by digestion with single-stranded-specific nuclease(s), andsize determination of the digested fragments. Two nucleic acid, or twopolypeptide sequences are substantially homologous to each other whenthe sequences exhibit at least about 70%-75%, preferably 80%-82%, morepreferably 85%-90%, even more preferably 92%, still more preferably 95%,and most preferably 98% sequence identity over a defined length of themolecules, as determined using the methods above. As used herein,substantially homologous also refers to sequences showing completeidentity to a specified DNA or polypeptide sequence. DNA sequences thatare substantially homologous can be identified in a Southernhybridization experiment under, for example, stringent conditions, asdefined for that particular system. Defining appropriate hybridizationconditions is known to those with skill of the art. See, e.g., Sambrooket al., supra; Nucleic Acid Hybridization: A Practical Approach, editorsB. D. Hames and S. J. Higgins, (1985) Oxford; Washington, D.C.; IRLPress).

Selective hybridization of two nucleic acid fragments can be determinedas follows. The degree of sequence identity between two nucleic acidmolecules affects the efficiency and strength of hybridization eventsbetween such molecules. A partially identical nucleic acid sequence willat least partially inhibit the hybridization of a completely identicalsequence to a target molecule. Inhibition of hybridization of thecompletely identical sequence can be assessed using hybridization assaysthat are well known in the art (e.g., Southern (DNA) blot, Northern(RNA) blot, solution hybridization, or the like, see Sambrook, et al.,Molecular Cloning: A Laboratory Manual, Second Edition, (1989) ColdSpring Harbor, N.Y.). Such assays can be conducted using varying degreesof selectivity, for example, using conditions varying from low to highstringency. If conditions of low stringency are employed, the absence ofnon-specific binding can be assessed using a secondary probe that lackseven a partial degree of sequence identity (for example, a probe havingless than about 30% sequence identity with the target molecule), suchthat, in the absence of non-specific binding events, the secondary probewill not hybridize to the target.

When utilizing a hybridization-based detection system, a nucleic acidprobe is chosen that is complementary to a reference nucleic acidsequence, and then by selection of appropriate conditions the probe andthe reference sequence selectively hybridize, or bind, to each other toform a duplex molecule. A nucleic acid molecule that is capable ofhybridizing selectively to a reference sequence under moderatelystringent hybridization conditions typically hybridizes under conditionsthat allow detection of a target nucleic acid sequence of at least about10-14 nucleotides in length having at least approximately 70% sequenceidentity with the sequence of the selected nucleic acid probe. Stringenthybridization conditions typically allow detection of target nucleicacid sequences of at least about 10-14 nucleotides in length having asequence identity of greater than about 90-95% with the sequence of theselected nucleic acid probe. Hybridization conditions useful forprobe/reference sequence hybridization, where the probe and referencesequence have a specific degree of sequence identity, can be determinedas is known in the art (see, for example, Nucleic Acid Hybridization: APractical Approach, editors B. D. Hames and S. J. Higgins, (1985)Oxford; Washington, D.C.; IRL Press).

Conditions for hybridization are well-known to those of skill in theart. Hybridization stringency refers to the degree to whichhybridization conditions disfavor the formation of hybrids containingmismatched nucleotides, with higher stringency correlated with a lowertolerance for mismatched hybrids. Factors that affect the stringency ofhybridization are well-known to those of skill in the art and include,but are not limited to, temperature, pH, ionic strength, andconcentration of organic solvents such as, for example, formamide anddimethylsulfoxide. As is known to those of skill in the art,hybridization stringency is increased by higher temperatures, lowerionic strength and lower solvent concentrations.

With respect to stringency conditions for hybridization, it is wellknown in the art that numerous equivalent conditions can be employed toestablish a particular stringency by varying, for example, the followingfactors: the length and nature of the probe sequences, base compositionof the various sequences, concentrations of salts and otherhybridization solution components, the presence or absence of blockingagents in the hybridization solutions (e.g., dextran sulfate, andpolyethylene glycol), hybridization reaction temperature and timeparameters, as well as, varying wash conditions. The selection of aparticular set of hybridization conditions is selected followingstandard methods in the art (see, for example, Sambrook, et al.,Molecular Cloning: A Laboratory Manual, Second Edition, (1989) ColdSpring Harbor, N.Y.).

“Recombination” refers to a process of exchange of genetic informationbetween two polynucleotides. For the purposes of this disclosure,“homologous recombination (HR)” refers to the specialized form of suchexchange that takes place, for example, during repair of double-strandbreaks in cells. This process requires nucleotide sequence homology,that uses a “donor” molecule to template repair of a “target” molecule(i.e., the one that experienced the double-strand break), and isvariously known as “non-crossover gene conversion” or “short tract geneconversion,” because it leads to the transfer of genetic informationfrom the donor to the target. Without wishing to be bound by anyparticular theory, such transfer can involve mismatch correction ofheteroduplex DNA that forms between the broken target and the donor,and/or “synthesis-dependent strand annealing,” in which the donor isused to resynthesize genetic information that will become part of thetarget, and/or related processes. Such specialized HR often results inan alteration of the sequence of the target molecule such that part orall of the sequence of the donor polynucleotide is incorporated into thetarget polynucleotide.

“Cleavage” refers to the breakage of the covalent backbone of a DNAmolecule. Cleavage can be initiated by a variety of methods including,but not limited to, enzymatic or chemical hydrolysis of a phosphodiesterbond. Both single-stranded cleavage and double-stranded cleavage arepossible, and double-stranded cleavage can occur as a result of twodistinct single-stranded cleavage events. DNA cleavage can result in theproduction of either blunt ends or staggered ends. In certainembodiments, fusion polypeptides are used for targeted double-strandedDNA cleavage.

A “cleavage domain” comprises one or more polypeptide sequences whichpossesses catalytic activity for DNA cleavage. A cleavage domain can becontained in a single polypeptide chain or cleavage activity can resultfrom the association of two (or more) polypeptides.

A “cleavage half-domain” is a polypeptide sequence which, in conjunctionwith a second polypeptide (either identical or different) forms acomplex having cleavage activity (preferably double-strand cleavageactivity).

An “engineered cleavage half-domain” is a cleavage half-domain that hasbeen modified so as to form obligate heterodimers with another cleavagehalf-domain (e.g., another engineered cleavage half-domain). See, also,U.S. Pat. Nos. 7,914,796; 8,034,598; 8,623,618 and U.S. PatentPublication No. 2011/0201055, incorporated herein by reference in theirentireties.

“Chromatin” is the nucleoprotein structure comprising the cellulargenome. Cellular chromatin comprises nucleic acid, primarily DNA, andprotein, including histones and non-histone chromosomal proteins. Themajority of eukaryotic cellular chromatin exists in the form ofnucleosomes, wherein a nucleosome core comprises approximately 150 basepairs of DNA associated with an octamer comprising two each of histonesH2A, H2B, H3 and H4; and linker DNA (of variable length depending on theorganism) extends between nucleosome cores. A molecule of histone H1 isgenerally associated with the linker DNA. For the purposes of thepresent disclosure, the term “chromatin” is meant to encompass all typesof cellular nucleoprotein, both prokaryotic and eukaryotic. Cellularchromatin includes both chromosomal and episomal chromatin.

A “chromosome,” is a chromatin complex comprising all or a portion ofthe genome of a cell. The genome of a cell is often characterized by itskaryotype, which is the collection of all the chromosomes that comprisethe genome of the cell. The genome of a cell can comprise one or morechromosomes.

An “episome” is a replicating nucleic acid, nucleoprotein complex orother structure comprising a nucleic acid that is not part of thechromosomal karyotype of a cell. Examples of episomes include plasmidsand certain viral genomes.

An “accessible region” is a site in cellular chromatin in which a targetsite present in the nucleic acid can be bound by an exogenous moleculewhich recognizes the target site. Without wishing to be bound by anyparticular theory, it is believed that an accessible region is one thatis not packaged into a nucleosomal structure. The distinct structure ofan accessible region can often be detected by its sensitivity tochemical and enzymatic probes, for example, nucleases.

A “target site” or “target sequence” is a nucleic acid sequence thatdefines a portion of a nucleic acid to which a binding molecule willbind, provided sufficient conditions for binding exist. For example, thesequence 5′-GAATTC-3′ is a target site for the Eco RI restrictionendonuclease. In addition Table 3 and 13 list the target sites for thebinding of the ZFP recognition helices of Table 2 and Table 12.

An “exogenous” molecule is a molecule that is not normally present in acell, but can be introduced into a cell by one or more genetic,biochemical or other methods. “Normal presence in the cell” isdetermined with respect to the particular developmental stage andenvironmental conditions of the cell. Thus, for example, a molecule thatis present in cells only during the early stages of development of aflower is an exogenous molecule with respect to the cells of a fullydeveloped flower. Similarly, a molecule induced by heat shock is anexogenous molecule with respect to a non-heat-shocked cell. An exogenousmolecule can comprise, for example, a coding sequence for anypolypeptide or fragment thereof, a functioning version of amalfunctioning endogenous molecule or a malfunctioning version of anormally-functioning endogenous molecule. Additionally, an exogenousmolecule can comprise a coding sequence from another species that is anortholog of an endogenous gene in the host cell.

An exogenous molecule can be, among other things, a small molecule, suchas is generated by a combinatorial chemistry process, or a macromoleculesuch as a protein, nucleic acid, carbohydrate, lipid, glycoprotein,lipoprotein, polysaccharide, any modified derivative of the abovemolecules, or any complex comprising one or more of the above molecules.Nucleic acids include DNA and RNA, can be single- or double-stranded;can be linear, branched or circular; and can be of any length. Nucleicacids include those capable of forming duplexes, as well astriplex-forming nucleic acids. See, for example, U.S. Pat. Nos.5,176,996 and 5,422,251. Proteins include, but are not limited to,DNA-binding proteins, transcription factors, chromatin remodelingfactors, methylated DNA binding proteins, polymerases, methylases,demethylases, acetylases, deacetylases, kinases, phosphatases,integrases, recombinases, ligases, topoisomerases, gyrases andhelicases. Thus, the term includes “transgenes” or “genes of interest”which are exogenous sequences introduced into a plant cell.

An exogenous molecule can be the same type of molecule as an endogenousmolecule, e.g., an exogenous protein or nucleic acid. For example, anexogenous nucleic acid can comprise an infecting viral genome, a plasmidor episome introduced into a cell, or a chromosome that is not normallypresent in the cell. Methods for the introduction of exogenous moleculesinto cells are known to those of skill in the art and include, but arenot limited to, protoplast transformation, silicon carbide (e.g.,WHISKERS™), Agrobacterium-mediated transformation, lipid-mediatedtransfer (i.e., liposomes, including neutral and cationic lipids),electroporation, direct injection, cell fusion, particle bombardment(e.g., using a “gene gun”), calcium phosphate co-precipitation,DEAE-dextran-mediated transfer and viral vector-mediated transfer.

By contrast, an “endogenous” molecule is one that is normally present ina particular cell at a particular developmental stage under particularenvironmental conditions. For example, an endogenous nucleic acid cancomprise a chromosome, the genome of a mitochondrion, chloroplast orother organelle, or a naturally-occurring episomal nucleic acid.Additional endogenous molecules can include proteins, for example,transcription factors and enzymes.

As used herein, the term “product of an exogenous nucleic acid” includesboth polynucleotide and polypeptide products, for example, transcriptionproducts (polynucleotides such as RNA) and translation products(polypeptides).

A “fusion” molecule is a molecule in which two or more subunit moleculesare linked, preferably covalently. The subunit molecules can be the samechemical type of molecule, or can be different chemical types ofmolecules. Examples of the first type of fusion molecule include, butare not limited to, fusion proteins, for example, a fusion between aDNA-binding domain (e.g., ZFP, TALE and/or meganuclease DNA-bindingdomains) and a nuclease (cleavage) domain (e.g., endonuclease,meganuclease, etc. and fusion nucleic acids (for example, a nucleic acidencoding the fusion protein described herein). Examples of the secondtype of fusion molecule include, but are not limited to, a fusionbetween a triplex-forming nucleic acid and a polypeptide, and a fusionbetween a minor groove binder and a nucleic acid.

Expression of a fusion protein in a cell can result from delivery of thefusion protein to the cell or by delivery of a polynucleotide encodingthe fusion protein to a cell, wherein the polynucleotide is transcribed,and the transcript is translated, to generate the fusion protein.Trans-splicing, polypeptide cleavage and polypeptide ligation can alsobe involved in expression of a protein in a cell. Methods forpolynucleotide and polypeptide delivery to cells are presented elsewherein this disclosure.

A “gene,” for the purposes of the present disclosure, includes a DNAregion encoding a gene product (see infra), as well as all DNA regionswhich regulate the production of the gene product, whether or not suchregulatory sequences are adjacent to coding and/or transcribedsequences. Accordingly, a gene includes, but is not necessarily limitedto, promoter sequences, terminators, translational regulatory sequencessuch as ribosome binding sites and internal ribosome entry sites,enhancers, silencers, insulators, boundary elements, replicationorigins, matrix attachment sites and locus control regions.

“Gene expression” refers to the conversion of the information, containedin a gene, into a gene product. A gene product can be the directtranscriptional product of a gene (e.g., mRNA, tRNA, rRNA, antisenseRNA, ribozyme, structural RNA or any other type of RNA) or a proteinproduced by translation of a mRNA. Gene products also include RNAs whichare modified, by processes such as capping, polyadenylation,methylation, and editing, and proteins modified by, for example,methylation, acetylation, phosphorylation, ubiquitination,ADP-ribosylation, myristoylation, and glycosylation.

“Modulation” of gene expression refers to a change in the activity of agene. Modulation of expression can include, but is not limited to, geneactivation and gene repression.

A “transgenic selectable marker” refers to an exogenous sequencecomprising a marker gene operably linked to a promoter and 3′-UTR tocomprise a chimeric gene expression cassette. Non-limiting examples oftransgenic selectable markers include herbicide tolerance, antibioticresistance, and visual reporter markers. The transgenic selectablemarker can be integrated along with a donor sequence via targetedintegration. As such, the transgenic selectable marker expresses aproduct that is used to assess integration of the donor. In contrast,the methods and compositions described herein allow for integration ofany donor sequence without the need for co-integration of a transgenicselectable marker, for example by using a donor which mutates theendogenous gene into which it is integrated to produce a selectablemarker (i.e., the selectable marker as used in this instance is nottransgenic) from the endogenous target locus. Non-limiting examples ofselectable markers include herbicide tolerance markers, including amutated AHAS gene as described herein.

“Plant” cells include, but are not limited to, cells of monocotyledonous(monocots) or dicotyledonous (dicots) plants. Non-limiting examples ofmonocots include cereal plants such as maize, rice, barley, oats, wheat,sorghum, rye, sugarcane, pineapple, onion, banana, and coconut.Non-limiting examples of dicots include tobacco, tomato, sunflower,cotton, sugarbeet, potato, lettuce, melon, soy, canola (rapeseed), andalfalfa. Plant cells may be from any part of the plant and/or from anystage of plant development.

A “region of interest” is any region of cellular chromatin, such as, forexample, a gene or a non-coding sequence within or adjacent to a gene,in which it is desirable to bind an exogenous molecule. Binding can befor the purposes of targeted DNA cleavage and/or targeted recombination.A region of interest can be present in a chromosome, an episome, anorganellar genome (e.g., mitochondrial, chloroplast), or an infectingviral genome, for example. A region of interest can be within the codingregion of a gene, within transcribed non-coding regions such as, forexample, leader sequences, trailer sequences or introns, or withinnon-transcribed regions, either upstream or downstream of the codingregion. A region of interest can be as small as a single nucleotide pairor up to 2,000 nucleotide pairs in length, or any integral value ofnucleotide pairs.

The terms “operative linkage” and “operatively linked” (or “operablylinked”) are used interchangeably with reference to a juxtaposition oftwo or more components (such as sequence elements), in which thecomponents are arranged such that both components function normally andallow the possibility that at least one of the components can mediate afunction that is exerted upon at least one of the other components. Byway of illustration, a transcriptional regulatory sequence, such as apromoter, is operatively linked to a coding sequence if thetranscriptional regulatory sequence controls the level of transcriptionof the coding sequence in response to the presence or absence of one ormore transcriptional regulatory factors. A transcriptional regulatorysequence is generally operatively linked in cis with a coding sequence,but need not be directly adjacent to it. For example, an enhancer is atranscriptional regulatory sequence that is operatively linked to acoding sequence, even though they are not contiguous.

With respect to fusion polypeptides, the term “operatively linked” canrefer to the fact that each of the components performs the same functionin linkage to the other component as it would if it were not so linked.For example, with respect to a fusion polypeptide in which a DNA-bindingdomain (ZFP, TALE) is fused to a cleavage domain (e.g., endonucleasedomain such as FokI, meganuclease domain, etc.), the DNA-binding domainand the cleavage domain are in operative linkage if, in the fusionpolypeptide, the DNA-binding domain portion is able to bind its targetsite and/or its binding site, while the cleavage (nuclease) domain isable to cleave DNA in the vicinity of the target site. The nucleasedomain may also exhibit DNA-binding capability (e.g., a nuclease fusedto a ZFP or TALE domain that also can bind to DNA). Similarly, withrespect to a fusion polypeptide in which a DNA-binding domain is fusedto an activation or repression domain, the DNA-binding domain and theactivation or repression domain are in operative linkage if, in thefusion polypeptide, the DNA-binding domain portion is able to bind itstarget site and/or its binding site, while the activation domain is ableto upregulate gene expression or the repression domain is able todownregulate gene expression. A “functional fragment” of a protein,polypeptide or nucleic acid is a protein, polypeptide or nucleic acidwhose sequence is not identical to the full-length protein, polypeptideor nucleic acid, yet retains the same function as the full-lengthprotein, polypeptide or nucleic acid. A functional fragment can possessmore, fewer, or the same number of residues as the corresponding nativemolecule, and/or can contain one or more amino acid or nucleotidesubstitutions. Methods for determining the function of a nucleic acid(e.g., coding function, ability to hybridize to another nucleic acid)are well-known in the art. Similarly, methods for determining proteinfunction are well-known. For example, the DNA-binding function of apolypeptide can be determined, for example, by filter-binding,electrophoretic mobility-shift, or immunoprecipitation assays. DNAcleavage can be assayed by gel electrophoresis. See Ausubel et al.,supra. The ability of a protein to interact with another protein can bedetermined, for example, by co-immunoprecipitation, two-hybrid assays orcomplementation, both genetic and biochemical. See, for example, Fieldset al. (1989) Nature 340:245-246; U.S. Pat. No. 5,585,245 and PCT WO98/44350.

DNA-Binding Domains

Any DNA-binding domain can be used in the methods disclosed herein. Incertain embodiments, the DNA binding domain comprises a zinc fingerprotein. A zinc finger binding domain comprises one or more zincfingers. Miller et al. (1985) EMBO J. 4:1609-1614; Rhodes (1993)Scientific American February: 56-65; U.S. Pat. No. 6,453,242. The zincfinger binding domains described herein generally include 2, 3, 4, 5, 6or even more zinc fingers.

Typically, a single zinc finger domain is about 30 amino acids inlength. Structural studies have demonstrated that each zinc fingerdomain (motif) contains two beta sheets (held in a beta turn whichcontains the two invariant cysteine residues) and an alpha helix(containing the two invariant histidine residues), which are held in aparticular conformation through coordination of a zinc atom by the twocysteines and the two histidines.

Zinc fingers include both canonical C₂H₂ zinc fingers (i.e., those inwhich the zinc ion is coordinated by two cysteine and two histidineresidues) and non-canonical zinc fingers such as, for example, C₃H zincfingers (those in which the zinc ion is coordinated by three cysteineresidues and one histidine residue) and C₄ zinc fingers (those in whichthe zinc ion is coordinated by four cysteine residues). See also WO02/057293 and also U.S. Patent Publication No. 20080182332 regardingnon-canonical ZFPs for use in plants.

An engineered zinc finger binding domain can have a novel bindingspecificity, compared to a naturally-occurring zinc finger protein.Engineering methods include, but are not limited to, rational design andvarious types of selection. Rational design includes, for example, usingdatabases comprising triplet (or quadruplet) nucleotide sequences andindividual zinc finger amino acid sequences, in which each triplet orquadruplet nucleotide sequence is associated with one or more amino acidsequences of zinc fingers which bind the particular triplet orquadruplet sequence.

Exemplary selection methods, including phage display and two-hybridsystems, are disclosed in U.S. Pat. Nos. 5,789,538; 5,925,523;6,007,988; 6,013,453; 6,410,248; 6,140,466; 6,200,759; and 6,242,568; aswell as WO 98/37186; WO 98/53057; WO 00/27878; WO 01/88197 and GB2,338,237.

Enhancement of binding specificity for zinc finger binding domains hasbeen described, for example, in U.S. Pat. No. 6,794,136.

Since an individual zinc finger binds to a three-nucleotide (i.e.,triplet) sequence (or a four-nucleotide sequence which can overlap, byone nucleotide, with the four-nucleotide binding site of an adjacentzinc finger), the length of a sequence to which a zinc finger bindingdomain is engineered to bind (e.g., a target sequence) will determinethe number of zinc fingers in an engineered zinc finger binding domain.For example, for ZFPs in which the finger motifs do not bind tooverlapping subsites, a six-nucleotide target sequence is bound by atwo-finger binding domain; a nine-nucleotide target sequence is bound bya three-finger binding domain, etc. As noted herein, binding sites forindividual zinc fingers (i.e., subsites) in a target site need not becontiguous, but can be separated by one or several nucleotides,depending on the length and nature of the amino acids sequences betweenthe zinc fingers (i.e., the inter-finger linkers) in a multi-fingerbinding domain.

In a multi-finger zinc finger binding domain, adjacent zinc fingers canbe separated by amino acid linker sequences of approximately 5 aminoacids (so-called “canonical” inter-finger linkers) or, alternatively, byone or more non-canonical linkers. See, e.g., U.S. Pat. Nos. 6,453,242and 6,534,261. For engineered zinc finger binding domains comprisingmore than three fingers, insertion of longer (“non-canonical”)inter-finger linkers between certain of the zinc fingers may bedesirable in some instances as it may increase the affinity and/orspecificity of binding by the binding domain. See, for example, U.S.Pat. No. 6,479,626 and WO 01/53480. Accordingly, multi-finger zincfinger binding domains can also be characterized with respect to thepresence and location of non-canonical inter-finger linkers. Forexample, a six-finger zinc finger binding domain comprising threefingers (joined by two canonical inter-finger linkers), a long linkerand three additional fingers (joined by two canonical inter-fingerlinkers) is denoted a 2×3 configuration. Similarly, a binding domaincomprising two fingers (with a canonical linker therebetween), a longlinker and two additional fingers (joined by a canonical linker) isdenoted a 2×2 configuration. A protein comprising three two-finger units(in each of which the two fingers are joined by a canonical linker), andin which each two-finger unit is joined to the adjacent two finger unitby a long linker, is referred to as a 3×2 configuration.

The presence of a long or non-canonical inter-finger linker between twoadjacent zinc fingers in a multi-finger binding domain often allows thetwo fingers to bind to subsites which are not immediately contiguous inthe target sequence. Accordingly, there can be gaps of one or morenucleotides between subsites in a target site; i.e., a target site cancontain one or more nucleotides that are not contacted by a zinc finger.For example, a 2×2 zinc finger binding domain can bind to twosix-nucleotide sequences separated by one nucleotide, i.e., it binds toa 13-nucleotide target site. See also Moore et al. (2001a) Proc. Natl.Acad. Sci. USA 98:1432-1436; Moore et al. (2001b) Proc. Natl. Acad. Sci.USA 98:1437-1441 and WO 01/53480.

As discussed previously, a target subsite is a three- or four-nucleotidesequence that is bound by a single zinc finger. For certain purposes, atwo-finger unit is denoted a “binding module.” A binding module can beobtained by, for example, selecting for two adjacent fingers in thecontext of a multi-finger protein (generally three fingers) which bind aparticular six-nucleotide target sequence. Alternatively, modules can beconstructed by assembly of individual zinc fingers. See also WO 98/53057and WO 01/53480.

Alternatively, the DNA-binding domain may be derived from a nuclease.For example, the recognition sequences of homing endonucleases andmeganucleases such as I-SceI, I-CeuI, PI-PspI, PI-Sce, I-SceIV, I-CsmI,I-PanI, I-SceII, I-PpoI, I-SceIII, I-CreI, I-TevI, I-TevII and I-TevIIIare known. See also U.S. Pat. No. 5,420,032; U.S. Pat. No. 6,833,252;Belfort et al. (1997) Nucleic Acids Res. 25:3379-3388; Dujon et al.(1989) Gene 82:115-118; Perler et al. (1994) Nucleic Acids Res. 22,1125-1127; Jasin (1996) Trends Genet. 12:224-228; Gimble et al. (1996)J. Mol. Biol. 263:163-180; Argast et al. (1998) J. Mol. Biol.280:345-353 and the New England Biolabs catalogue. In addition, theDNA-binding specificity of homing endonucleases and meganucleases can beengineered to bind non-natural target sites. See, for example, Chevalieret al. (2002) Molec. Cell 10:895-905; Epinat et al. (2003) Nucleic AcidsRes. 31:2952-2962; Ashworth et al. (2006) Nature 441:656-659; Paques etal. (2007) Current Gene Therapy 7:49-66; U.S. Patent Publication No.20070117128. The DNA-binding domains of the homing endonucleases andmeganucleases may be altered in the context of the nuclease as a whole(i.e., such that the nuclease includes the cognate cleavage domain) ormay be fused to a heterologous DNA-binding domain (e.g., zinc fingerprotein or TALE) or to a heterologous cleavage domain. DNA-bindingdomains derived from meganucleases may also exhibit DNA-bindingactivity.

In other embodiments, the DNA-binding domain comprises a naturallyoccurring or engineered (non-naturally occurring) TAL effector DNAbinding domain. See, e.g., U.S. Pat. No. 8,586,526, incorporated byreference in its entirety herein. The plant pathogenic bacteria of thegenus Xanthomonas are known to cause many diseases in important cropplants. Pathogenicity of Xanthomonas depends on a conserved type IIIsecretion (T3S) system which injects more than 25 different effectorproteins into the plant cell. Among these injected proteins aretranscription activator-like effectors (TALE) which mimic planttranscriptional activators and manipulate the plant transcriptome (seeKay et al (2007) Science 318:648-651). These proteins contain a DNAbinding domain and a transcriptional activation domain. One of the mostwell characterized TALEs is AvrBs3 from Xanthomonas campestgris pv.Vesicatoria (see Bonas et al (1989) Mol Gen Genet 218: 127-136 andWO2010079430). TALEs contain a centralized domain of tandem repeats,each repeat containing approximately 34 amino acids, which are key tothe DNA binding specificity of these proteins. In addition, they containa nuclear localization sequence and an acidic transcriptional activationdomain (for a review see Schornack S, et al (2006) J Plant Physiol163(3): 256-272). In addition, in the phytopathogenic bacteria Ralstoniasolanacearum two genes, designated brg11 and hpx17 have been found thatare homologous to the AvrBs3 family of Xanthomonas in the R.solanacearum biovar 1 strain GMI1000 and in the biovar 4 strain RS1000(See Heuer et al (2007) Appland Envir Micro 73(13): 4379-4384). Thesegenes are 98.9% identical in nucleotide sequence to each other butdiffer by a deletion of 1,575 bp in the repeat domain of hpx17. However,both gene products have less than 40% sequence identity with AvrBs3family proteins of Xanthomonas.

Thus, in some embodiments, the DNA binding domain that binds to a targetsite in a target locus is an engineered domain from a TAL effectorsimilar to those derived from the plant pathogens Xanthomonas (see Bochet al, (2009) Science 326: 1509-1512 and Moscou and Bogdanove, (2009)Science 326: 1501) and Ralstonia (see Heuer et al (2007) Applied andEnvironmental Microbiology 73(13): 4379-4384); U.S. Pat. Nos. 8,586,526;8,420,782 and 8,440,431. TALENs may include C-cap and/or N-cap sequences(e.g., C-terminal and/or N-terminal truncations of the TALE backbone(e.g., “+17”, “+63” C-caps). See, e.g., U.S. Pat. No. 8,586,526.

As another alternative, the DNA-binding domain may be derived from aleucine zipper protein. Leucine zippers are a class of proteins that areinvolved in protein-protein interactions in many eukaryotic regulatoryproteins that are important transcriptional factors associated with geneexpression. The leucine zipper refers to a common structural motifshared in these transcriptional factors across several kingdomsincluding animals, plants, yeasts, etc. The leucine zipper is formed bytwo polypeptides (homodimer or heterodimer) that bind to specific DNAsequences in a manner where the leucine residues are evenly spacedthrough an α-helix, such that the leucine residues of the twopolypeptides end up on the same face of the helix. The DNA bindingspecificity of leucine zippers can be utilized in the DNA-bindingdomains disclosed herein.

Cleavage Domains

As noted above, any DNA-binding domain may be associated with a cleavage(nuclease) domain. For example, homing endonucleases may be modified intheir DNA-binding specificity while retaining nuclease function. Inaddition, zinc finger proteins may also be fused to a nuclease(cleavage) domain to form a zinc finger nuclease (ZFN). TALE proteinsmay be linked to a nuclease (cleavage) domain to form a TALEN.

The cleavage domain portion of the fusion proteins disclosed herein canbe obtained from any endonuclease or exonuclease. Exemplaryendonucleases from which a cleavage domain can be derived include, butare not limited to, restriction endonucleases and homing endonucleases.See, for example, 2002-2003 Catalogue, New England Biolabs, Beverly,Mass.; and Belfort et al. (1997) Nucleic Acids Res. 25:3379-3388.Additional enzymes which cleave DNA are known (e.g., S1 Nuclease; mungbean nuclease; pancreatic DNase I; micrococcal nuclease; yeast HOendonuclease; see also Linn et al. (eds.) Nucleases, Cold Spring HarborLaboratory Press, 1993). Non limiting examples of homing endonucleasesand meganucleases include I-SceI, I-CeuI, PI-PspI, PI-Sce, I-SceIV,I-CsmI, I-PanI, I-SceII, I-PpoI, I-SceIII, I-CreI, I-TevI, I-TevII andI-TevIII are known. See also U.S. Pat. No. 5,420,032; U.S. Pat. No.6,833,252; Belfort et al. (1997) Nucleic Acids Res. 25:3379-3388; Dujonet al. (1989) Gene 82:115-118; Perler et al. (1994) Nucleic Acids Res.22, 1125-1127; Jasin (1996) Trends Genet. 12:224-228; Gimble et al.(1996) J. Mol. Biol. 263:163-180; Argast et al. (1998) J. Mol. Biol.280:345-353 and the New England Biolabs catalogue. One or more of theseenzymes (or functional fragments thereof) can be used as a source ofcleavage domains and cleavage half-domains.

Restriction endonucleases (restriction enzymes) are present in manyspecies and are capable of sequence-specific binding to DNA (at arecognition site), and cleaving DNA at or near the site of binding.Certain restriction enzymes (e.g., Type IIS) cleave DNA at sites removedfrom the recognition site and have separable binding and cleavagedomains. For example, the Type IIS enzyme FokI catalyzes double-strandedcleavage of DNA, at 9 nucleotides from its recognition site on onestrand and 13 nucleotides from its recognition site on the other. See,for example, U.S. Pat. Nos. 5,356,802; 5,436,150 and 5,487,994; as wellas Li et al. (1992) Proc. Natl. Acad. Sci. USA 89:4275-4279; Li et al.(1993) Proc. Natl. Acad. Sci. USA 90:2764-2768; Kim et al. (1994a) Proc.Natl. Acad. Sci. USA 91:883-887; Kim et al. (1994b) J. Biol. Chem.269:31,978-31,982. Thus, in one embodiment, fusion proteins comprise thecleavage domain (or cleavage half-domain) from at least one Type IISrestriction enzyme and one or more zinc finger binding domains, whichmay or may not be engineered.

An exemplary Type IIS restriction enzyme, whose cleavage domain isseparable from the binding domain, is FokI. This particular enzyme isactive as a dimer. Bitinaite et al. (1998) Proc. Natl. Acad. Sci. USA95: 10,570-10,575. Accordingly, for the purposes of the presentdisclosure, the portion of the FokI enzyme used in the disclosed fusionproteins is considered a cleavage half-domain. Thus, for targeteddouble-stranded cleavage and/or targeted replacement of cellularsequences using zinc finger-FokI fusions, two fusion proteins, eachcomprising a FokI cleavage half-domain, can be used to reconstitute acatalytically active cleavage domain. Alternatively, a singlepolypeptide molecule containing a zinc finger binding domain and twoFokI cleavage half-domains can also be used. Parameters for targetedcleavage and targeted sequence alteration using zinc finger-FokI fusionsare provided elsewhere in this disclosure.

A cleavage domain or cleavage half-domain can be any portion of aprotein that retains cleavage activity, or that retains the ability tomultimerize (e.g., dimerize) to form a functional cleavage domain.

Exemplary Type IIS restriction enzymes are described in U.S. PublicationNo. 20070134796, incorporated by reference herein in its entirety.

To enhance cleavage specificity, cleavage domains may also be modified.In certain embodiments, variants of the cleavage half-domain areemployed these variants minimize or prevent homodimerization of thecleavage half-domains. Amino acid residues at positions 446, 447, 479,483, 484, 486, 487, 490, 491, 496, 498, 499, 500, 531, 534, 537, and 538of FokI are all targets for influencing dimerization of the FokIcleavage half-domains. Non-limiting examples of such modified cleavagehalf-domains are described in detail in U.S. Pat. Nos. 7,888,121;7,914,796 and 8,034,598, incorporated by reference herein. See, also,Examples.

Additional engineered cleavage half-domains of FokI that form obligateheterodimers can also be used in the ZFNs described herein. Exemplaryengineered cleavage half-domains of Fok I that form obligateheterodimers include a pair in which a first cleavage half-domainincludes mutations at amino acid residues at positions 490 and 538 ofFok I and a second cleavage half-domain includes mutations at amino acidresidues 486 and 499.

Thus, in one embodiment, a mutation at 490 replaces Glu (E) with Lys(K); the mutation at 538 replaces Iso (I) with Lys (K); the mutation at486 replaced Gln (Q) with Glu (E); and the mutation at position 499replaces Iso (I) with Lys (K). Specifically, the engineered cleavagehalf-domains described herein were prepared by mutating positions 490(E→K) and 538 (I→K) in one cleavage half-domain to produce an engineeredcleavage half-domain designated “E490K:I538K” and by mutating positions486 (Q→E) and 499 (I→L) in another cleavage half-domain to produce anengineered cleavage half-domain designated “Q486E:I499L”. The engineeredcleavage half-domains described herein are obligate heterodimer mutantsin which aberrant cleavage is minimized or abolished. See, e.g., U.S.Pat. Nos. 7,914,796 and 8,034,598, the disclosures of which areincorporated by reference for all purposes. In certain embodiments, theengineered cleavage half-domain comprises mutations at positions 486,499 and 496 (numbered relative to wild-type FokI), for instancemutations that replace the wild type Gln (Q) residue at position 486with a Glu (E) residue, the wild type Iso (I) residue at position 499with a Leu (L) residue and the wild-type Asn (N) residue at position 496with an Asp (D) or Glu (E) residue (also referred to as a “ELD” and“ELE” domains, respectively). In other embodiments, the engineeredcleavage half-domain comprises mutations at positions 490, 538 and 537(numbered relative to wild-type FokI), for instance mutations thatreplace the wild type Glu (E) residue at position 490 with a Lys (K)residue, the wild type Iso (I) residue at position 538 with a Lys (K)residue, and the wild-type His (H) residue at position 537 with a Lys(K) residue or a Arg (R) residue (also referred to as “KKK” and “KKR”domains, respectively). In other embodiments, the engineered cleavagehalf-domain comprises mutations at positions 490 and 537 (numberedrelative to wild-type FokI), for instance mutations that replace thewild type Glu (E) residue at position 490 with a Lys (K) residue and thewild-type His (H) residue at position 537 with a Lys (K) residue or aArg (R) residue (also referred to as “KIK” and “KIR” domains,respectively). (See U.S. Patent Publication No. 20110201055). In otherembodiments, the engineered cleavage half domain comprises the “Sharkey”and/or “Sharkey'” mutations (see Guo et al, (2010) J. Mol. Biol.400(1):96-107).

Engineered cleavage half-domains described herein can be prepared usingany suitable method, for example, by site-directed mutagenesis ofwild-type cleavage half-domains (Fok I) as described in U.S. Pat. Nos.7,914,796; 8,034,598 and 8,623,618; and U.S. Patent Publication No.20110201055.

In other embodiments, the nuclease comprises an engineered TALEDNA-binding domain and a nuclease domain (e.g., endonuclease and/ormeganuclease domain), also referred to as TALENs. Methods andcompositions for engineering these TALEN proteins for robust, sitespecific interaction with the target sequence of the user's choosinghave been published (see U.S. Pat. No. 8,586,526). In some embodiments,the TALEN comprises a endonuclease (e.g., FokI) cleavage domain orcleavage half-domain. In other embodiments, the TALE-nuclease is a megaTAL. These mega TAL nucleases are fusion proteins comprising a TALE DNAbinding domain and a meganuclease cleavage domain. The meganucleasecleavage domain is active as a monomer and does not require dimerizationfor activity. (See Boissel et al., (2013) Nucl Acid Res: 1-13, doi:10.1093/nar/gkt1224). In addition, the nuclease domain may also exhibitDNA-binding functionality.

In still further embodiments, the nuclease comprises a compact TALEN(cTALEN). These are single chain fusion proteins linking a TALE DNAbinding domain to a TevI nuclease domain. The fusion protein can act aseither a nickase localized by the TALE region, or can create a doublestrand break, depending upon where the TALE DNA binding domain islocated with respect to the TevI nuclease domain (see Beurdeley et al(2013) Nat Comm: 1-8 DOI: 10.1038/ncomms2782). Any TALENs may be used incombination with additional TALENs (e.g., one or more TALENs (cTALENs orFokI-TALENs) with one or more mega-TALs).

Nucleases may be assembled using standard techniques, including in vivoat the nucleic acid target site using so-called “split-enzyme”technology (see e.g. U.S. Patent Publication No. 20090068164).Components of such split enzymes may be expressed either on separateexpression constructs, or can be linked in one open reading frame wherethe individual components are separated, for example, by a self-cleaving2A peptide or IRES sequence. Components may be individual zinc fingerbinding domains or domains of a meganuclease nucleic acid bindingdomain.

Nucleases can be screened for activity prior to use, for example in ayeast-based chromosomal system as described in U.S. Pat. No. 8,563,314.Nuclease expression constructs can be readily designed using methodsknown in the art. See, e.g., United States Patent Publications20030232410; 20050208489; 20050026157; 20050064474; 20060188987;20060063231; and International Publication WO 07/014,275. Expression ofthe nuclease may be under the control of a constitutive promoter or aninducible promoter, for example the galactokinase promoter which isactivated (de-repressed) in the presence of raffinose and/or galactoseand repressed in presence of glucose.

In certain embodiments, the nuclease comprises a CRISPR/Cas system. TheCRISPR (clustered regularly interspaced short palindromic repeats)locus, which encodes RNA components of the system, and the cas(CRISPR-associated) locus, which encodes proteins (Jansen et al., 2002.Mol. Microbiol. 43: 1565-1575; Makarova et al., 2002. Nucleic Acids Res.30: 482-496; Makarova et al., 2006. Biol. Direct 1: 7; Haft et al.,2005. PLoS Comput. Biol. 1: e60) make up the gene sequences of theCRISPR/Cas nuclease system. CRISPR loci in microbial hosts contain acombination of CRISPR-associated (Cas) genes as well as non-coding RNAelements capable of programming the specificity of the CRISPR-mediatednucleic acid cleavage.

The Type II CRISPR is one of the most well characterized systems andcarries out targeted DNA double-strand break in four sequential steps.First, two non-coding RNA, the pre-crRNA array and tracrRNA, aretranscribed from the CRISPR locus. Second, tracrRNA hybridizes to therepeat regions of the pre-crRNA and mediates the processing of pre-crRNAinto mature crRNAs containing individual spacer sequences. Third, themature crRNA:tracrRNA complex directs Cas9 to the target DNA viaWatson-Crick base-pairing between the spacer on the crRNA and theprotospacer on the target DNA next to the protospacer adjacent motif(PAM), an additional requirement for target recognition. Finally, Cas9mediates cleavage of target DNA to create a double-stranded break withinthe protospacer. Activity of the CRISPR/Cas system comprises of threesteps: (i) insertion of foreign DNA sequences into the CRISPR array toprevent future attacks, in a process called ‘adaptation’, (ii)expression of the relevant proteins, as well as expression andprocessing of the array, followed by (iii) RNA-mediated interferencewith the foreign nucleic acid. Thus, in the bacterial cell, several ofthe so-called ‘Cas’ proteins are involved with the natural function ofthe CRISPR/Cas system and serve roles in functions such as insertion ofthe foreign DNA etc.

In certain embodiments, Cas protein may be a “functional derivative” ofa naturally occurring Cas protein. A “functional derivative” of a nativesequence polypeptide is a compound having a qualitative biologicalproperty in common with a native sequence polypeptide. “Functionalderivatives” include, but are not limited to, fragments of a nativesequence and derivatives of a native sequence polypeptide and itsfragments, provided that they have a biological activity in common witha corresponding native sequence polypeptide. A biological activitycontemplated herein is the ability of the functional derivative tohydrolyze a DNA substrate into fragments. The term “derivative”encompasses both amino acid sequence variants of polypeptide, covalentmodifications, and fusions thereof. Suitable derivatives of a Caspolypeptide or a fragment thereof include but are not limited tomutants, fusions, covalent modifications of Cas protein or a fragmentthereof. Cas protein, which includes Cas protein or a fragment thereof,as well as derivatives of Cas protein or a fragment thereof, may beobtainable from a cell or synthesized chemically or by a combination ofthese two procedures. The cell may be a cell that naturally produces Casprotein, or a cell that naturally produces Cas protein and isgenetically engineered to produce the endogenous Cas protein at a higherexpression level or to produce a Cas protein from an exogenouslyintroduced nucleic acid, which nucleic acid encodes a Cas that is sameor different from the endogenous Cas. In some case, the cell does notnaturally produce Cas protein and is genetically engineered to produce aCas protein. See, e.g., U.S. Provisional Application No. 61/823,689.

Thus, the nuclease comprises a DNA-binding domain in that specificallybinds to a target site in any gene in combination with a nuclease domainthat cleaves DNA at or near the binding site.

Fusion Proteins

Methods for design and construction of fusion proteins (andpolynucleotides encoding same) are known to those of skill in the art.For example, methods for the design and construction of fusion proteinscomprising DNA-binding domains (e.g., zinc finger domains, TALEs) andregulatory or cleavage domains (or cleavage half-domains), andpolynucleotides encoding such fusion proteins, are described in U.S.Pat. Nos. 8,586,526; 8,592,645; 8,399,218; 8,329,986; 7,888,121;6,453,242; and 6,534,261 and U.S. Patent Application Publications2007/0134796 and, herein incorporated by reference in their entireties.In certain embodiments, polynucleotides encoding the fusion proteins areconstructed. These polynucleotides can be inserted into a vector and thevector can be introduced into a cell (see below for additionaldisclosure regarding vectors and methods for introducing polynucleotidesinto cells).

In certain embodiments of the methods described herein, a zinc fingernuclease or TALEN comprises a fusion protein comprising a zinc fingerbinding domain or a TALE DNA binding domain and a nuclease domain (e.g.,Type IIS restriction enzyme and/or meganuclease domain). In certainembodiments, the ZFN or TALEN comprise a cleavage half-domain from theFokI restriction enzyme, and two such fusion proteins are expressed in acell. Expression of two fusion proteins in a cell can result fromdelivery of the two proteins to the cell; delivery of one protein andone nucleic acid encoding one of the proteins to the cell; delivery oftwo nucleic acids, each encoding one of the proteins, to the cell; or bydelivery of a single nucleic acid, encoding both proteins, to the cell.In additional embodiments, a fusion protein comprises a singlepolypeptide chain comprising two cleavage half domains and a zinc fingeror TALE binding domain. In this case, a single fusion protein isexpressed in a cell and, without wishing to be bound by theory, isbelieved to cleave DNA as a result of formation of an intramoleculardimer of the cleavage half-domains.

In certain embodiments, the components of the fusion proteins (e.g.,ZFP-FokI fusions) are arranged such that the DNA-binding domain isnearest the amino terminus of the fusion protein, and the cleavagehalf-domain is nearest the carboxy-terminus. This mirrors the relativeorientation of the cleavage domain in naturally-occurring dimerizingcleavage domains such as those derived from the FokI enzyme, in whichthe DNA-binding domain is nearest the amino terminus and the cleavagehalf-domain is nearest the carboxy terminus. In these embodiments,dimerization of the cleavage half-domains to form a functional nucleaseis brought about by binding of the fusion proteins to sites on oppositeDNA strands, with the 5′ ends of the binding sites being proximal toeach other.

In additional embodiments, the components of the fusion proteins (e.g.,ZFP-FokI fusions) are arranged such that the cleavage half-domain isnearest the amino terminus of the fusion protein, and the zinc fingerdomain is nearest the carboxy-terminus. In these embodiments,dimerization of the cleavage half-domains to form a functional nucleaseis brought about by binding of the fusion proteins to sites on oppositeDNA strands, with the 3′ ends of the binding sites being proximal toeach other.

In yet additional embodiments, a first fusion protein contains thecleavage half-domain nearest the amino terminus of the fusion protein,and the zinc finger domain nearest the carboxy-terminus, and a secondfusion protein is arranged such that the zinc finger domain is nearestthe amino terminus of the fusion protein, and the cleavage half-domainis nearest the carboxy-terminus. In these embodiments, both fusionproteins bind to the same DNA strand, with the binding site of the firstfusion protein containing the zinc finger domain nearest the carboxyterminus located to the 5′ side of the binding site of the second fusionprotein containing the zinc finger domain nearest the amino terminus.

In certain embodiments of the disclosed fusion proteins, the amino acidsequence between the zinc finger domain and the cleavage domain (orcleavage half-domain) is denoted the “ZC linker.” The ZC linker is to bedistinguished from the inter-finger linkers discussed above. See, e.g.,U.S. Pat. No. 7,888,121 for details on obtaining ZC linkers thatoptimize cleavage.

In one embodiment, the disclosure provides a ZFN comprising a zincfinger protein having one or more of the recognition helix amino acidsequences shown in Table 2 (e.g., a zinc finger protein made up ofcomponent zinc finger domains with the recognition helices as shown in asingle row of Table 2). In another embodiment, provided herein is a ZFPexpression vector comprising a nucleotide sequence encoding a ZFP havingone or more recognition helices shown in Tables 2 or 12. In anotherembodiment, provided herein is a ZFP that binds to a target site asshown in Tables 3 or 13 or a polynucleotide encoding a ZFP that binds toa target site shown in Tables 3 or 13.

Target Sites

The disclosed methods and compositions include fusion proteinscomprising a DNA-binding domain (e.g., ZFP, TALE, etc.) and a regulatorydomain or cleavage (e.g., nuclease) domain (or a cleavage half-domain),in which the DNA-binding domain, by binding to a sequence in cellularchromatin in one or more plant genes, induces cleavage and targetedintegration of one or more exogenous sequences (including transgenes)into the vicinity of the target sequence.

As set forth elsewhere in this disclosure, a DNA-binding domain can beengineered to bind to virtually any desired sequence. Accordingly, afteridentifying a region of interest containing a sequence at which generegulation, cleavage, or recombination is desired, one or moreDNA-binding domains can be engineered to bind to one or more sequencesin the region of interest. In certain embodiments, the DNA-bindingdomain comprises a zinc finger protein that binds to a target site inone or more AHAS genes as shown in Table 3 or Table 13.

Selection of a target site in a genomic region of interest in cellularchromatin of any gene for binding by a DNA-binding domain (e.g., atarget site) can be accomplished, for example, according to the methodsdisclosed in U.S. Pat. No. 6,453,242. It will be clear to those skilledin the art that simple visual inspection of a nucleotide sequence canalso be used for selection of a target site. Accordingly, any means fortarget site selection can be used in the claimed methods.

Target sites are generally composed of a plurality of adjacent targetsubsites. In the case of zinc finger proteins, a target subsite refersto the sequence (usually either a nucleotide triplet, or a nucleotidequadruplet that can overlap by one nucleotide with an adjacentquadruplet) bound by an individual zinc finger. See, for example, U.S.Pat. No. 6,794,136. If the strand with which a zinc finger protein makesmost contacts is designated the target strand “primary recognitionstrand,” or “primary contact strand,” some zinc finger proteins bind toa three base triplet in the target strand and a fourth base on thenon-target strand. A target site generally has a length of at least 9nucleotides and, accordingly, is bound by a zinc finger binding domaincomprising at least three zinc fingers. However binding of, for example,a 4-finger binding domain to a 12-nucleotide target site, a 5-fingerbinding domain to a 15-nucleotide target site or a 6-finger bindingdomain to an 18-nucleotide target site, is also possible. As will beapparent, binding of larger binding domains (e.g., 7-, 8-, 9-finger andmore) to longer target sites is also possible.

It is not necessary for a target site to be a multiple of threenucleotides. For example, in cases in which cross-strand interactionsoccur (see, e.g., U.S. Pat. Nos. 6,453,242 and 6,794,136), one or moreof the individual zinc fingers of a multi-finger binding domain can bindto overlapping quadruplet subsites. As a result, a three-finger proteincan bind a 10-nucleotide sequence, wherein the tenth nucleotide is partof a quadruplet bound by a terminal finger, a four-finger protein canbind a 13-nucleotide sequence, wherein the thirteenth nucleotide is partof a quadruplet bound by a terminal finger, etc.

In certain embodiments, the target site is in an AHAS locus (includinguntranslated regions such as the 3′ untranslated region of AHAS).Non-limiting examples of suitable AHAS target sites are shown in Table 3and Table 13. The AHAS (also known as AHAS/ALS) genes are present in allmajor plant species including but not limited to maize, soybean, cotton,Arabidopsis, rice, sunflower, wheat, barley, sugarbeet and Brassica.Specific amino acid modifications to the AHAS structural gene sequencehave been described that alter the resulting proteins sensitivity tovarious structural classes of herbicides without a negative penalty onplant performance. For example, imidazolinone-tolerant maize (Zea maysL.) [Currie R S, Kwon C S and Penner D, Magnitude of imazethapyrresistance of corn (Zea mays) hybrids with altered acetolactatesynthase. Weed Sci 43:578-582 (1995), Wright T R and Penner D, Corn (Zeamays) acetolactate synthase sensitivity to four classes ofALS-inhibiting herbicides. Weed Sci 46:8-12 (1998), Siehl D L, BengtsonA S, Brockman J P, Butler J H, Kraatz G W, Lamoreaux R J and SubramanianM V, Patterns of cross tolerance to herbicides inhibitingacetohydroxyacid synthase in commercial corn hybrids designed fortolerance to imidazolinones. Crop Sci 36:274-278 (1996), and Bailey W Aand Wilcut J W, Tolerance of imidazolinone-resistant corn (Zea mays) todiclosulam. Weed Technol 17:60-64 (2003)], rice (Oryza sativa L.)[Webster E P and Masson J A, Acetolactate synthase-inhibiting herbicideson imidazolinone-tolerant rice. Weed Sci 49:652-657 (2001) and, Gealy DR, Mitten D H and Rutger J N, Gene flow between red rice (Oryza sativa)and herbicide-resistant rice (O. sativa): implications for weedmanagement. Weed Technol 17:627-645 (2003)], bread wheat (Triticumaestivum L.) [Newhouse K, Smith W A, Starrett M A, Schaefer T J andSingh B K, Tolerance to imidazolinone herbicides in wheat. Plant Physiol100:882-886 (1992), and Pozniak C J and Hucl P J, Genetic analysis ofimidazolinone resistance in mutation-derived lines of common wheat. CropSci 44:23-30 (2004)], and oilseed rape (Brassica napus and B. juncea L.Czern.) [Shaner D L, Bascomb N F and Smith W, Imidazolinoneresistantcrops: selection, characterization and management, in Herbicideresistant crops, edited by Duke S O, CRC Press, Boca Raton, pp 143-157(1996) and Swanson E B, Herrgesell M J, Arnoldo M, Sippell D W and WongR S C, Microspore mutagenesis and selection: canola plants with fieldtolerance to the imidazolinones. Theor Appl Genet 78:525-530 (1989)],were developed through mutagenesis, selection, and conventional breedingtechnologies and have been commercialized since 1992, 2003, 2002, and1996, respectively. Several AHAS genes encoding AHAS enzymes that aretolerant to imidazolinone herbicides have been discovered in plants asnaturally occurring mutations and through the process ofchemically-induced mutagenesis. The S653N mutation is among the fivemost common single-point mutations in AHAS genes that result intolerance to imidazolinone herbicides in plants (Tan, S., Evans, R. R.,Dahmer, M. L., Singh, B. K., and Shaner, D. L. (2005)Imidazolinone-tolerant crops: History, current status and future. PestManag. Sci. 61:246-257).

The length and nature of amino acid linker sequences between individualzinc fingers in a multi-finger binding domain also affects binding to atarget sequence. For example, the presence of a so-called “non-canonicallinker,” “long linker” or “structured linker” between adjacent zincfingers in a multi-finger binding domain can allow those fingers to bindsubsites which are not immediately adjacent. Non-limiting examples ofsuch linkers are described, for example, in U.S. Pat. Nos. 6,479,626 and7,851,216. Accordingly, one or more subsites, in a target site for azinc finger binding domain, can be separated from each other by 1, 2, 3,4, 5 or more nucleotides. To provide but one example, a four-fingerbinding domain can bind to a 13-nucleotide target site comprising, insequence, two contiguous 3-nucleotide subsites, an interveningnucleotide, and two contiguous triplet subsites. See, also, U.S. PatentPublication Nos. 20090305419 and 20110287512 for compositions andmethods for linking artificial nucleases to bind to target sitesseparated by different numbers of nucleotides. Distance betweensequences (e.g., target sites) refers to the number of nucleotides ornucleotide pairs intervening between two sequences, as measured from theedges of the sequences nearest each other.

In certain embodiments, DNA-binding domains with transcription factorfunction are designed, for example by constructing fusion proteinscomprising a DNA-binding domain (e.g., ZFP or TALE) and atranscriptional regulatory domain (e.g., activation or repressiondomain). For transcription factor function, simple binding andsufficient proximity to the promoter are all that is generally needed.Exact positioning relative to the promoter, orientation, and withinlimits, distance does not matter greatly. This feature allowsconsiderable flexibility in choosing target sites for constructingartificial transcription factors. The target site recognized by theDNA-binding domain therefore can be any suitable site in the target genethat will allow activation or repression of gene expression, optionallylinked to a regulatory domain. Preferred target sites include regionsadjacent to, downstream, or upstream of the transcription start site. Inaddition, target sites that are located in enhancer regions, repressorsites, RNA polymerase pause sites, and specific regulatory sites (e.g.,SP-1 sites, hypoxia response elements, nuclear receptor recognitionelements, p53 binding sites), sites in the cDNA encoding region or in anexpressed sequence tag (EST) coding region.

In other embodiments, ZFPs with nuclease activity are designed.Expression of a ZFN comprising a fusion protein comprising a zinc fingerbinding domain and a cleavage domain (or of two fusion proteins, eachcomprising a zinc finger binding domain and a cleavage half-domain), ina cell, effects cleavage in the vicinity of the target sequence. Incertain embodiments, cleavage depends on the binding of two zinc fingerdomain/cleavage half-domain fusion molecules to separate target sites.The two target sites can be on opposite DNA strands, or alternatively,both target sites can be on the same DNA strand.

A variety of assays can be used to determine whether a ZFP modulatesgene expression. The activity of a particular ZFP can be assessed usinga variety of in vitro and in vivo assays, by measuring, e.g., protein ormRNA levels, product levels, enzyme activity, transcriptional activationor repression of a reporter gene, using, e.g., immunoassays (e.g., ELISAand immunohistochemical assays with antibodies), hybridization assays(e.g., RNase protection, northerns, in situ hybridization,oligonucleotide array studies), colorimetric assays, amplificationassays, enzyme activity assays, phenotypic assays, and the like.

ZFPs are typically first tested for activity in vitro using ELISA assaysand then using a yeast expression system. The ZFP is often first testedusing a transient expression system with a reporter gene, and thenregulation of the target endogenous gene is tested in cells and in wholeplants, both in vivo and ex vivo. The ZFP can be recombinantly expressedin a cell, recombinantly expressed in cells transplanted into a plant,or recombinantly expressed in a transgenic plant, as well asadministered as a protein to plant or cell using delivery vehiclesdescribed below. The cells can be immobilized, be in solution, beinjected into a plant, or be naturally occurring in a transgenic ornon-transgenic plant.

Transgenic and non-transgenic plants are also used as a preferredembodiment for examining regulation of endogenous gene expression invivo. Transgenic plants can stably express the ZFP of choice.Alternatively, plants that transiently express the ZFP of choice, or towhich the ZFP has been administered in a delivery vehicle, can be used.Regulation of endogenous gene expression is tested using any one of theassays described herein.

Methods for Targeted Cleavage

The disclosed methods and compositions can be used to cleave DNA at aregion of interest in cellular chromatin (e.g., at a desired orpredetermined site in a genome, for example, within or adjacent to anAHAS gene). For such targeted DNA cleavage, a DNA-binding domain (e.g.,zinc finger protein or TALE) is engineered to bind a target site at ornear the predetermined cleavage site, and a fusion protein comprisingthe engineered zinc finger binding domain and a cleavage domain isexpressed in a cell. Upon binding of the DNA-binding portion of thefusion protein to the target site, the DNA is cleaved near the targetsite by the cleavage domain.

Alternatively, two fusion proteins, each comprising a DNA-binding domainand a cleavage half-domain, are expressed in a cell, and bind to targetsites which are juxtaposed in such a way that a functional cleavagedomain is reconstituted and DNA is cleaved in the vicinity of the targetsites. In one embodiment, cleavage occurs between the target sites ofthe two DNA-binding domains. One or both of the zinc finger bindingdomains can be engineered.

For targeted cleavage using a zinc finger binding domain-cleavage domainfusion polypeptide, the binding site can encompass the cleavage site, orthe near edge of the binding site can be 1, 2, 3, 4, 5, 6, 10, 25, 50 ormore nucleotides (or any integral value between 1 and 50 nucleotides)from the cleavage site. The exact location of the binding site, withrespect to the cleavage site, will depend upon the particular cleavagedomain, and the length of the ZC linker. For methods in which two fusionpolypeptides, each comprising a zinc finger binding domain and acleavage half-domain, are used, the binding sites generally straddle thecleavage site. Thus the near edge of the first binding site can be 1, 2,3, 4, 5, 6, 10, 25 or more nucleotides (or any integral value between 1and 50 nucleotides) on one side of the cleavage site, and the near edgeof the second binding site can be 1, 2, 3, 4, 5, 6, 10, 25 or morenucleotides (or any integral value between 1 and 50 nucleotides) on theother side of the cleavage site. Methods for mapping cleavage sites invitro and in vivo are known to those of skill in the art.

Thus, the methods described herein can employ an engineered zinc fingerbinding domain fused to a cleavage domain. In these cases, the bindingdomain is engineered to bind to a target sequence, at or near wherecleavage is desired. The fusion protein, or a polynucleotide encodingsame, is introduced into a plant cell. Once introduced into, orexpressed in, the cell, the fusion protein binds to the target sequenceand cleaves at or near the target sequence. The exact site of cleavagedepends on the nature of the cleavage domain and/or the presence and/ornature of linker sequences between the binding and cleavage domains. Incases where two fusion proteins, each comprising a cleavage half-domain,are used, the distance between the near edges of the binding sites canbe 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25 or more nucleotides (or anyintegral value between 1 and 50 nucleotides). Optimal levels of cleavagecan also depend on both the distance between the binding sites of thetwo fusion proteins (see, for example, Smith et al. (2000) Nucleic AcidsRes. 28:3361-3369; Bibikova et al. (2001) Mol. Cell. Biol. 21:289-297)and the length of the ZC linker in each fusion protein. See, also, U.S.Patent Publication 20050064474A1 and International Patent PublicationsWO05/084190, WO05/014791 and WO03/080809.

In certain embodiments, the cleavage domain comprises two cleavagehalf-domains, both of which are part of a single polypeptide comprisinga binding domain, a first cleavage half-domain and a second cleavagehalf-domain. The cleavage half-domains can have the same amino acidsequence or different amino acid sequences, so long as they function tocleave the DNA.

Cleavage half-domains may also be provided in separate molecules. Forexample, two fusion polypeptides may be introduced into a cell, whereineach polypeptide comprises a binding domain and a cleavage half-domain.The cleavage half-domains can have the same amino acid sequence ordifferent amino acid sequences, so long as they function to cleave theDNA. Further, the binding domains bind to target sequences which aretypically disposed in such a way that, upon binding of the fusionpolypeptides, the two cleavage half-domains are presented in a spatialorientation to each other that allows reconstitution of a cleavagedomain (e.g., by dimerization of the half-domains), thereby positioningthe half-domains relative to each other to form a functional cleavagedomain, resulting in cleavage of cellular chromatin in a region ofinterest. Generally, cleavage by the reconstituted cleavage domainoccurs at a site located between the two target sequences. One or bothof the proteins can be engineered to bind to its target site.

The two fusion proteins can bind in the region of interest in the sameor opposite polarity, and their binding sites (i.e., target sites) canbe separated by any number of nucleotides, e.g., from 0 to 200nucleotides or any integral value therebetween. In certain embodiments,the binding sites for two fusion proteins, each comprising a zinc fingerbinding domain and a cleavage half-domain, can be located between 5 and18 nucleotides apart, for example, 5-8 nucleotides apart, or 15-18nucleotides apart, or 6 nucleotides apart, or 16 nucleotides apart, asmeasured from the edge of each binding site nearest the other bindingsite, and cleavage occurs between the binding sites.

The site at which the DNA is cleaved generally lies between the bindingsites for the two fusion proteins. Double-strand breakage of DNA oftenresults from two single-strand breaks, or “nicks,” offset by 1, 2, 3, 4,5, 6 or more nucleotides, (for example, cleavage of double-stranded DNAby native Fok I results from single-strand breaks offset by 4nucleotides). Thus, cleavage does not necessarily occur at exactlyopposite sites on each DNA strand. In addition, the structure of thefusion proteins and the distance between the target sites can influencewhether cleavage occurs adjacent a single nucleotide pair, or whethercleavage occurs at several sites. However, for many applications,including targeted recombination and targeted mutagenesis (see infra)cleavage within a range of nucleotides is generally sufficient, andcleavage between particular base pairs is not required.

As noted above, the fusion protein(s) can be introduced as polypeptidesand/or polynucleotides. For example, two polynucleotides, eachcomprising sequences encoding one of the aforementioned polypeptides,can be introduced into a cell, and when the polypeptides are expressedand each binds to its target sequence, cleavage occurs at or near thetarget sequence. Alternatively, a single polynucleotide comprisingsequences encoding both fusion polypeptides is introduced into a cell.Polynucleotides can be DNA, RNA or any modified forms or analogues orDNA and/or RNA.

To enhance cleavage specificity, additional compositions may also beemployed in the methods described herein. For example, single cleavagehalf-domains can exhibit limited double-stranded cleavage activity. Inmethods in which two fusion proteins, each containing a three-fingerzinc finger domain and a cleavage half-domain, are introduced into thecell, either protein specifies an approximately 9-nucleotide targetsite. Although the aggregate target sequence of 18 nucleotides is likelyto be unique in a mammalian and plant genomes, any given 9-nucleotidetarget site occurs, on average, approximately 23,000 times in the humangenome. Thus, non-specific cleavage, due to the site-specific binding ofa single half-domain, may occur. Accordingly, the methods describedherein contemplate the use of a dominant-negative mutant of a nuclease(or a nucleic acid encoding same) that is expressed in a cell along withthe two fusion proteins. The dominant-negative mutant is capable ofdimerizing but is unable to induce double-stranded cleavage whendimerized. By providing the dominant-negative mutant in molar excess tothe fusion proteins, only regions in which both fusion proteins arebound will have a high enough local concentration of functional cleavagehalf-domains for dimerization and double-stranded cleavage to occur.

In other embodiments, the nuclease domain(s) are nickases in that theyinduce single-stranded break. In certain embodiments, the nickasecomprises two nucleases domains one of which is modified (e.g., to becatalytically inactive) such that the nuclease makes only asingle-stranded break. Such nickases are described for example in U.S.Patent Publication No. 20100047805. Two nickases may be used to induce adouble-stranded break.

Expression Vectors

A nucleic acid encoding one or more fusion proteins (e.g., ZFNs, TALENs,etc.) as described herein can be cloned into a vector for transformationinto prokaryotic or eukaryotic cells for replication and/or expression.Vectors can be prokaryotic vectors (e.g., plasmids, or shuttle vectors,insect vectors) or eukaryotic vectors. A nucleic acid encoding a fusionprotein can also be cloned into an expression vector, for administrationto a cell.

To express the fusion proteins, sequences encoding the fusion proteinsare typically subcloned into an expression vector that contains apromoter to direct transcription. Suitable prokaryotic and eukaryoticpromoters are well known in the art and described, e.g., in Sambrook etal., Molecular Cloning, A Laboratory Manual (2nd ed. 1989; 3^(rd) ed.,2001); Kriegler, Gene Transfer and Expression: A Laboratory Manual(1990); and Current Protocols in Molecular Biology (Ausubel et al.,supra. Bacterial expression systems for expressing the ZFP are availablein, e.g., E. coli, Bacillus sp., and Salmonella (Palva et al., Gene22:229-235 (1983)). Kits for such expression systems are commerciallyavailable. Eukaryotic expression systems for mammalian cells, yeast, andinsect cells are well known by those of skill in the art and are alsocommercially available.

The promoter used to direct expression of a fusion protein-encodingnucleic acid depends on the particular application. For example, astrong constitutive promoter suited to the host cell is typically usedfor expression and purification of fusion proteins.

In contrast, when a fusion protein is administered in vivo forregulation of a plant gene (see, “Nucleic Acid Delivery to Plant Cells”section below), either a constitutive, regulated (e.g., duringdevelopment, by tissue or cell type, or by the environment) or aninducible promoter is used, depending on the particular use of thefusion protein. Non-limiting examples of plant promoters includepromoter sequences derived from A. thaliana ubiquitin-3 (ubi-3) (Callis,et al., 1990, J. Biol. Chem. 265-12486-12493); A. tumefaciens mannopinesynthase (Δmas) (Petolino et al., U.S. Pat. No. 6,730,824); and/orCassava Vein Mosaic Virus (CsVMV) (Verdaguer et al., 1996, PlantMolecular Biology 31:1129-1139). See, also, Examples.

In addition to the promoter, the expression vector typically contains atranscription unit or expression cassette that contains all theadditional elements required for the expression of the nucleic acid inhost cells, either prokaryotic or eukaryotic. A typical expressioncassette thus contains a promoter (comprising ribosome binding sites)operably linked, e.g., to a nucleic acid sequence encoding the fusionprotein, and signals required, e.g., for efficient polyadenylation ofthe transcript, transcriptional termination, or translation termination.Additional elements of the cassette may include, e.g., enhancers,heterologous splicing signals, the 2A sequence from Thosea asigna virus(Mattion et al. (1996) J. Virol. 70:8124-8127), and/or a nuclearlocalization signal (NLS).

The particular expression vector used to transport the geneticinformation into the cell is selected with regard to the intended use ofthe fusion proteins, e.g., expression in plants, animals, bacteria,fungus, protozoa, etc. (see expression vectors described below).Standard bacterial and animal expression vectors are known in the artand are described in detail, for example, U.S. Patent Publication20050064474A1 and International Patent Publications WO 05/084190, WO05/014791 and WO 03/080809.

Standard transfection methods can be used to produce bacterial, plant,mammalian, yeast or insect cell lines that express large quantities ofprotein, which can then be purified using standard techniques (see,e.g., Colley et al., J. Biol. Chem. 264:17619-17622 (1989); Guide toProtein Purification, in Methods in Enzymology, vol. 182 (Deutscher,ed., 1990)). Transformation of eukaryotic and prokaryotic cells areperformed according to standard techniques (see, e.g., Morrison, J.Bact. 132:349-351 (1977); Clark-Curtiss & Curtiss, Methods in Enzymology101:347-362 (Wu et al., eds., 1983).

Any of the well-known procedures for introducing foreign nucleotidesequences into such host cells may be used. These include the use ofcalcium phosphate transfection, polybrene, protoplast fusion,electroporation, ultrasonic methods (e.g., sonoporation), liposomes,microinjection, naked DNA, plasmid vectors, viral vectors,Agrobacterium-mediated transformation, silicon carbide (e.g., WHISKERS™)mediated transformation, both episomal and integrative, and any of theother well-known methods for introducing cloned genomic DNA, cDNA,synthetic DNA or other foreign genetic material into a host cell (see,e.g., Sambrook et al., supra). It is only necessary that the particulargenetic engineering procedure used be capable of successfullyintroducing at least one gene into the host cell capable of expressingthe protein of choice.

Donors

As noted above, insertion of one or more exogenous sequence (also calleda “donor sequence” or “donor” or “transgene”), for example for stackingcan also be completed. A donor sequence can contain a non-homologoussequence flanked by two regions of homology to allow for efficient HDRat the location of interest. Additionally, donor sequences can comprisea vector molecule containing sequences that are not homologous to theregion of interest in cellular chromatin. A donor molecule can containseveral, discontinuous regions of homology to cellular chromatin. Forexample, for targeted insertion of sequences not normally present in aregion of interest, said sequences can be present in a donor nucleicacid molecule and flanked by regions of homology to sequence in theregion of interest.

The donor polynucleotide can be DNA or RNA, single-stranded ordouble-stranded and can be introduced into a cell in linear or circularform. See, e.g., U.S. Patent Publication Nos. 20100047805; 20110281361;and 20110207221. If introduced in linear form, the ends of the donorsequence can be protected (e.g., from exonucleolytic degradation) bymethods known to those of skill in the art. For example, one or moredideoxynucleotide residues are added to the 3′ terminus of a linearmolecule and/or self-complementary oligonucleotides are ligated to oneor both ends. See, for example, Chang et al. (1987) Proc. Natl. Acad.Sci. USA 84:4959-4963; Nehls et al. (1996) Science 272:886-889.Additional methods for protecting exogenous polynucleotides fromdegradation include, but are not limited to, addition of terminal aminogroup(s) and the use of modified internucleotide linkages such as, forexample, phosphorothioates, phosphoramidates, and O-methyl ribose ordeoxyribose residues.

A polynucleotide can be introduced into a cell as part of a vectormolecule having additional sequences such as, for example, replicationorigins, promoters and genes encoding antibiotic resistance. Moreover,donor polynucleotides can be introduced as naked nucleic acid, asnucleic acid complexed with an agent such as a liposome or poloxamer, orcan be delivered by viruses (e.g., adenovirus, AAV, herpesvirus,retrovirus, lentivirus and integrase defective lentivirus (IDLY)). See,e.g., U.S. Patent Publication No. 20090117617.

The donor is generally inserted so that its expression is driven by theendogenous promoter at the integration site, namely the promoter thatdrives expression of the endogenous gene into which the donor isinserted. However, it will be apparent that the donor may comprise apromoter and/or enhancer, for example a constitutive promoter or aninducible or tissue specific promoter. Furthermore, the donor moleculemay be inserted into an endogenous gene such that all, some or none ofthe endogenous gene is expressed.

Furthermore, although not required for expression, exogenous sequencesmay also include transcriptional or translational regulatory sequences,for example, promoters, enhancers, insulators, internal ribosome entrysites, sequences encoding 2A peptides and/or polyadenylation signals.

The donor sequence is introduced into an endogenous gene (or multiplealleles of the gene) such that the function of the endogenous gene isaltered to act as an endogenous marker for transgene integration,thereby resulting in a genomic modification. In certain embodiments, theendogenous locus into which the transgene(s) is (are) introduced is anAHAS locus. Several mutations in the AHAS gene are known to confer GroupB, or ALS inhibitor herbicide tolerance (for example imidazolinone orsulfonylurea), including a single mutation of serine at position 653 toasparagine (S653N). See, e.g., Lee et al. (2011) Proc. Nat'l. Acad. Sci.USA 108: 8909-8913, and Tan, S., Evans, R. R., Dahmer, M. L., Singh, B.K., and Shaner, D. L. (2005) Imidazolinone-tolerant crops: History,current status and future. Pest Manag. Sci. 61:246-257.

AHAS is one desirable locus because the gene is transcriptionally activeat all stages of plant development, it is not prone to gene silencing(e.g., by DNA, Histone Methylation, iRNA, etc.), where the insertion ofa new gene or plant transformation unit into this locus does not have anegative impact on the agronomic or quality properties of the hostplant. The ubiquitous nature of the AHAS locus and clear commercialevidence that alteration AHAS locus or loci in canola, corn, sunflower,cotton, soybean, sugar beet, wheat, and any other plant does not carryan agronomic or quality penalty means the AHAS loci represents broadclass of a preferred target loci across all commercially relevant plantspecies.

Integration of the donor DNA into the wild type (herbicide susceptible)AHAS locus typically both introduces an exogenous sequence (e.g., atransgene) and a mutation to the endogenous AHAS to produce a genomicmodification that confers tolerance to imidazolinones (i.e., a productthat results in an herbicide tolerant plant cell), thus allowingregeneration of correctly targeted plants using an endogenousimidazolinone selection system rather than a transgenic selection markersystem. Stacking of a second transgene at the AHAS locus can be achievedby integration of a donor DNA that introduces one or more additionaltransgenes, confers susceptibility to imidazolines but tolerance tosulfonylureas (i.e., a product that results in an herbicide tolerantplant cell), thus allowing regeneration of correctly targeted plantsusing a sulfonylurea selection agent. Stacking of a third transgene canbe achieved by integration of a donor DNA that introduces furthertransgene(s) and confers susceptibility to sulfonylurea and tolerance toimidazolinones, thus allowing regeneration of correctly targeted plantsusing an imidazolinone selection agent. As such, continued rounds ofsequential transgene stacking are possible by the use of donor moleculesthat introduce mutations (e.g., genomic modification) to wild-type AHASthus allowing differential cycling between sulfonylurea andimidazolinone chemical selection agents.

Nucleic Acid Delivery to Plant Cells

As noted above, DNA constructs (e.g., nuclease(s) and/or donor(s)) maybe introduced into (e.g., into the genome of) a desired plant host by avariety of conventional techniques. For reviews of such techniques see,for example, Weissbach & Weissbach Methods for Plant Molecular Biology(1988, Academic Press, N.Y.) Section VIII, pp. 421-463; and Grierson &Corey, Plant Molecular Biology (1988, 2d Ed.), Blackie, London, Ch. 7-9.See, also, U.S. Patent Publication Nos. 20090205083; 20100199389;20110167521 and 20110189775, incorporated herein by reference in theirentireties. It will be apparent that one or more DNA constructs can beemployed in the practice of the present invention, for example thenuclease(s) may be carried by the same construct or different constructsas the construct(s) carrying the donor(s).

The DNA construct(s) may be introduced directly into the genomic DNA ofthe plant cell using techniques such as electroporation andmicroinjection of plant cell protoplasts, or the DNA constructs can beintroduced directly to plant tissue using biolistic methods, such as DNAparticle bombardment (see, e.g., Klein et al. (1987) Nature 327:70-73).Alternatively, the DNA construct can be introduced into the plant cellvia nanoparticle transformation (see, e.g., U.S. Patent Publication No.20090104700, which is incorporated herein by reference in its entirety).Alternatively, the DNA constructs may be combined with suitable T-DNAborder/flanking regions and introduced into a conventional Agrobacteriumtumefaciens host vector. Agrobacterium tumefaciens-mediatedtransformation techniques, including disarming of oncogenes and thedevelopment and use of binary vectors, are well described in thescientific literature. See, for example Horsch et al. (1984) Science233:496-498, and Fraley et al. (1983) Proc. Nat'l. Acad. Sci. USA80:4803.

In addition, gene transfer may be achieved using non-Agrobacteriumbacteria or viruses such as Rhizobium sp. NGR234, Sinorhizoboiummeliloti, Mesorhizobium loti, potato virus X, cauliflower mosaic virusand cassava vein mosaic virus and/or tobacco mosaic virus, See, e.g.,Chung et al. (2006)Trends Plant Sci. 11(1):1-4.

The virulence functions of the Agrobacterium tumefaciens host willdirect the insertion of a T-strand containing the construct and adjacentmarker into the plant cell DNA when the cell is infected by the bacteriausing binary T-DNA vector (Bevan (1984) Nuc. Acid Res. 12:8711-8721) orthe co-cultivation procedure (Horsch et al. (1985) Science227:1229-1231). Generally, the Agrobacterium transformation system isused to engineer dicotyledonous plants (Bevan et al. (1982) Ann. Rev.Genet 16:357-384; Rogers et al. (1986) Methods Enzymol. 118:627-641).The Agrobacterium transformation system may also be used to transform,as well as transfer, DNA to monocotyledonous plants and plant cells. SeeU.S. Pat. No. 5,591,616; Hernalsteen et al. (1984) EMBO J 3:3039-3041;Hooykass-Van Slogteren et al. (1984) Nature 311:763-764; Grimsley et al.(1987) Nature 325:1677-179; Boulton et al. (1989) Plant Mol. Biol.12:31-40; and Gould et al. (1991) Plant Physiol. 95:426-434.

Alternative gene transfer and transformation methods include, but arenot limited to, protoplast transformation through calcium-, polyethyleneglycol (PEG)- or electroporation-mediated uptake of naked DNA (seePaszkowski et al. (1984) EMBO J 3:2717-2722, Potrykus et al. (1985)Molec. Gen. Genet. 199:169-177; Fromm et al. (1985) Proc. Nat. Acad.Sci. USA 82:5824-5828; and Shimamoto (1989) Nature 338:274-276) andelectroporation of plant tissues (D'Halluin et al. (1992) Plant Cell4:1495-1505). Additional methods for plant cell transformation includemicroinjection, silicon carbide (e.g., WHISKERS™) mediated DNA uptake(Kaeppler et al. (1990) Plant Cell Reporter 9:415-418), andmicroprojectile bombardment (see Klein et al. (1988) Proc. Nat. Acad.Sci. USA 85:4305-4309; and Gordon-Kamm et al. (1990) Plant Cell2:603-618). Finally, nanoparticles, nanocarriers and cell penetratingpeptides can be utilized to deliver DNA, RNA, peptides and/or proteinsinto plant cells (see WO/2011/26644, WO/2009/046384, andWO/2008/148223).

The disclosed methods and compositions can be used to insert exogenoussequences into an AHAS gene. This is useful inasmuch as expression of anintroduced transgene into a plant genome depends critically on itsintegration site and, as noted above, AHAS provides a suitable site fortransgene integration. Accordingly, genes encoding, e.g., herbicidetolerance, insect resistance, nutrients, antibiotics or therapeuticmolecules can be inserted, by targeted recombination, into regions of aplant genome favorable to their expression.

Transformed plant cells which are produced by any of the abovetransformation techniques can be cultured to regenerate a whole plantwhich possesses the transformed genotype and thus the desired phenotype.Such regeneration techniques rely on manipulation of certainphytohormones in a tissue culture growth medium, typically relying on abiocide and/or herbicide marker which has been introduced together withthe desired nucleotide sequences. Plant regeneration from culturedprotoplasts is described in Evans, et al., “Protoplasts Isolation andCulture” in Handbook of Plant Cell Culture, pp. 124-176, MacmillanPublishing Company, New York, 1983; and Binding, Regeneration of Plants,Plant Protoplasts, pp. 21-73, CRC Press, Boca Raton, 1985. Regenerationcan also be obtained from plant callus, explants, organs, pollens,embryos or parts thereof. Such regeneration techniques are describedgenerally in Klee et al. (1987) Ann. Rev. of Plant Phys. 38:467-486.

Nucleic acids introduced into a plant cell can be used to confer desiredtraits on essentially any plant. A wide variety of plants and plant cellsystems may be engineered for the desired physiological and agronomiccharacteristics described herein using the nucleic acid constructs ofthe present disclosure and the various transformation methods mentionedabove. In preferred embodiments, target plants and plant cells forengineering include, but are not limited to, those monocotyledonous anddicotyledonous plants, such as crops including grain crops (e.g., wheat,maize, rice, millet, barley), fruit crops (e.g., tomato, apple, pear,strawberry, orange), forage crops (e.g., alfalfa), root vegetable crops(e.g., carrot, potato, sugar beets, yam), leafy vegetable crops (e.g.,lettuce, spinach); flowering plants (e.g., petunia, rose,chrysanthemum), conifers and pine trees (e.g., pine fir, spruce); plantsused in phytoremediation (e.g., heavy metal accumulating plants); oilcrops (e.g., sunflower, rape seed) and plants used for experimentalpurposes (e.g., Arabidopsis). Thus, the disclosed methods andcompositions have use over a broad range of plants, including, but notlimited to, species from the genera Asparagus, Avena, Brassica, Citrus,Citrullus, Capsicum, Cucurbita, Daucus, Erigeron, Glycine, Gossypium,Hordeum, Lactuca, Lolium, Lycopersicon, Malus, Manihot, Nicotiana,Orychophragmus, Oryza, Persea, Phaseolus, Pisum, Pyrus, Prunus,Raphanus, Secale, Solanum, Sorghum, Triticum, Vitis, Vigna, and Zea.

The introduction of nucleic acids introduced into a plant cell can beused to confer desired traits on essentially any plant. In certainembodiments, the integrated transgene(s) in plant cells results inplants having increased amount of fruit yield, increased biomass ofplant (or fruit of the plant), higher content of fruit flesh,concentrated fruit set, larger plants, increased fresh weight, increaseddry weight, increased solids context, higher total weight at harvest,enhanced intensity and/or uniformity of color of the crop, alteredchemical (e.g., oil, fatty acid, carbohydrate, protein) characteristics,etc.

One with skill in the art will recognize that an exogenous sequence canbe transiently incorporated into a plant cell. The introduction of anexogenous polynucleotide sequence can utilize the cell machinery of theplant cell in which the sequence has been introduced. The expression ofan exogenous polynucleotide sequence comprising a ZFN that istransiently incorporated into a plant cell can be assayed by analyzingthe genomic DNA of the target sequence to identify and determine anyindels, inversions, or insertions. These types of rearrangements resultfrom the cleavage of the target site within the genomic DNA sequence,and the subsequent DNA repair. In addition, the expression of anexogenous polynucleotide sequence can be assayed using methods whichallow for the testing of marker gene expression known to those ofordinary skill in the art. Transient expression of marker genes has beenreported using a variety of plants, tissues, and DNA delivery systems.Transient analyses systems include but are not limited to direct genedelivery via electroporation or particle bombardment of tissues in anytransient plant assay using any plant species of interest. Suchtransient systems would include but are not limited to electroporationof protoplasts from a variety of tissue sources or particle bombardmentof specific tissues of interest. The present disclosure encompasses theuse of any transient expression system to evaluate a site specificendonuclease (e.g., ZFN) and to introduce transgenes and/or mutationswithin a target gene (e.g., AHAS) to result in a genomic modification.Examples of plant tissues envisioned to test in transients via anappropriate delivery system would include but are not limited to leafbase tissues, callus, cotyledons, roots, endosperm, embryos, floraltissue, pollen, and epidermal tissue.

One of skill in the art will recognize that an exogenous polynucleotidesequence can be stably incorporated in transgenic plants. Once theexogenous polynucleotide sequence is confirmed to be operable, it can beintroduced into other plants by sexual crossing. Any of a number ofstandard breeding techniques can be used, depending upon the species tobe crossed.

A transformed plant cell, callus, tissue or plant may be identified andisolated by selecting or screening the engineered plant material for aphenotype encoded by the markers present on the exogenous DNA sequence.Markers may also be described and referred to as selectable markers, orreporter markers. The markers can be utilized for the identification andselection of transformed plants (“transformants”). Typically, the markeris incorporated into the genome of a plant cell as an exogenoussequence. In some examples, the exogenous marker sequence isincorporated into the plant genome at a site specific target loci as adonor sequence, wherein the donor sequence contains mutations whichresult in tolerance to a selection agent (e.g., herbicides, etc.). Inother examples, the exogenous marker sequence is incorporated into theplant genome as a transgene (i.e., “transgenic selectable marker”),wherein the marker gene is operably linked to a promoter and 3′-UTR tocomprise a chimeric gene expression cassette. The expression of themarker gene results in expression of a visual marker protein or intolerance to a selection agent (e.g., herbicide, antibiotics, etc.).

For instance, selection can be performed by growing the engineered plantmaterial on media containing an inhibitory amount of the antibiotic orherbicide (i.e., also described as a selective agent) to which thetransforming gene construct confers tolerance. In an embodiment,selectable marker genes include herbicide tolerance genes.

Herbicide tolerance markers code for a modified target proteininsensitive to the herbicide, or for an enzyme that degrades anddetoxifies the herbicide in the plant before it can act. For example, amodified target protein insensitive to an herbicide would includetolerance to glyphosate. Plants tolerant to glyphosate have beenobtained by using genes coding for mutant target enzyme5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). Genes and mutantsfor EPSPS are well known, and include mutant5-enolpyruvylshikimate-3-phosphate synthase (EPSPs), dgt-28, and aroAgenes. Such genes provide tolerance to glyphosate via the introductionof recombinant nucleic acids and/or various forms of in vivo mutagenesisof the native EPSPs genes. An example of enzymes that degrade anddetoxify herbicides in the plant would include tolerance to glufosinateammonium, bromoxynil, and 2,4-dichlorophenoxyacetate (2,4-D). Toleranceto these herbicides has been obtained by expressing bacterial genes thatencode pat or DSM-2, a nitrilase, an aad-1 or an aad-12 gene within aplant cell as a transgene. Tolerance genes for phosphono compoundsinclude bar and pat genes from Streptomyces species, includingStreptomyces hygroscopicus and Streptomyces viridichromogenes, andpyridinoxy or phenoxy proprionic acids and cyclohexones (ACCaseinhibitor-encoding genes). Exemplary genes conferring tolerance tocyclohexanediones and/or aryloxyphenoxypropanoic acid (includingHaloxyfop, Diclofop, Fenoxyprop, Fluazifop, Quizalofop) include genes ofacetyl coenzyme A carboxylase (ACCase), such as; Accl-S1, Accl-S2 andAccl-S3. In an embodiment, herbicides can inhibit photosynthesis,including triazine (psbA and ls+ genes) or benzonitrile (nitrilasegene). Other herbicide tolerant gene sequences are known by those withskill in the art.

Antibiotic resistant markers code for an enzyme that degrades anddetoxifies an antibiotic in the plant before it can act on the plant.Various types of antibiotics are known that can impede plant growth anddevelopment when used at proper concentrations, such as kanamycin,chloramphenicol, spectinomycin, and hygromycin. Exogenous sequences canbe obtained (e.g., bacterial genes) and expressed as a transgene tobreakdown the antibiotic. For example, antibiotic resistant marker genesinclude exogenous sequences encoding antibiotic resistance, such as thegenes encoding neomycin phosphotransferase II (NEO), chloramphenicolacetyltransferase (CAT), alkaline phosphatase, spectinomycin resistance,kanamycin resistance, and hygromycin phosphotransferase (HPT).

Further, transformed plants and plant cells can also be identified byscreening for the activities of a reporter gene that encode a visiblemarker gene. Reporter genes are typically provided as recombinantnucleic acid constructs and integrated into the plant cell as atransgene. Visual observation of proteins such as reporter genesencoding β-glucuronidase (GUS), luciferase, green fluorescent protein(GFP), yellow fluorescent protein (YFP), DsRed, β-galactosidase may beused to identify and select transformants. Such selection and screeningmethodologies are well known to those skilled in the art.

The above list of marker genes is not meant to be limiting. Any reporteror selectable marker gene is encompassed by the present disclosure.Moreover, it should be appreciated that markers (e.g., herbicidetolerant markers) are primarily utilized for the identification andselection of transformed plants, as compared to a trait (e.g., herbicidetolerant traits) that are utilized for providing tolerance to herbicidesapplied in a field environment to control weed species.

Physical and biochemical methods also may be used to identify plant orplant cell transformants containing stably inserted gene constructs, orplant cell containing target gene altered genomic DNA which results fromthe transient expression of a site-specific endonuclease (e.g., ZFN).These methods include but are not limited to: 1) Southern analysis orPCR amplification for detecting and determining the structure of therecombinant DNA insert; 2) Northern blot, 51 RNase protection,primer-extension or reverse transcriptase-PCR amplification fordetecting and examining RNA transcripts of the gene constructs; 3)enzymatic assays for detecting enzyme or ribozyme activity, where suchgene products are encoded by the gene construct; 4) protein gelelectrophoresis, Western blot techniques, immunoprecipitation, orenzyme-linked immunoassays (ELISA), where the gene construct productsare proteins. Additional techniques, such as in situ hybridization,enzyme staining, and immunostaining, also may be used to detect thepresence or expression of the recombinant construct in specific plantorgans and tissues. The methods for doing all these assays are wellknown to those skilled in the art.

Effects of gene manipulation using the methods disclosed herein can beobserved by, for example, northern blots of the RNA (e.g., mRNA)isolated from the tissues of interest. Typically, if the mRNA is presentor the amount of mRNA has increased, it can be assumed that thecorresponding transgene is being expressed. Other methods of measuringgene and/or encoded polypeptide activity can be used. Different types ofenzymatic assays can be used, depending on the substrate used and themethod of detecting the increase or decrease of a reaction product orby-product. In addition, the levels of polypeptide expressed can bemeasured immunochemically, i.e., ELISA, RIA, EIA and other antibodybased assays well known to those of skill in the art, such as byelectrophoretic detection assays (either with staining or westernblotting). As one non-limiting example, the detection of the AAD-1 andPAT proteins using an ELISA assay is described in U.S. PatentPublication No. 20090093366, which reference is hereby incorporated byreference in its entirety herein. A transgene may be selectivelyexpressed in some tissues of the plant or at some developmental stages,or the transgene may be expressed in substantially all plant tissues,substantially along its entire life cycle. However, any combinatorialexpression mode is also applicable.

The present disclosure also encompasses seeds of the transgenic plantsdescribed above wherein the seed has the transgene or gene construct.The present disclosure further encompasses the progeny, clones, celllines or cells of the transgenic plants described above wherein saidprogeny, clone, cell line or cell has the transgene or gene construct.

Fusion proteins (e.g., ZFNs) and expression vectors encoding fusionproteins can be administered directly to the plant for gene regulation,targeted cleavage, and/or recombination. In certain embodiments, theplant contains multiple paralogous target genes. For example, for AHAS,Brassica napus includes 5 paralogs and wheat includes 3 paralogs. Thus,one or more different fusion proteins or expression vectors encodingfusion proteins may be administered to a plant in order to target one ormore of these paralogous genes in the plant.

Administration of effective amounts is by any of the routes normallyused for introducing fusion proteins into ultimate contact with theplant cell to be treated. The ZFPs are administered in any suitablemanner, preferably with acceptable carriers. Suitable methods ofadministering such modulators are available and well known to those ofskill in the art, and, although more than one route can be used toadminister a particular composition, a particular route can oftenprovide a more immediate and more effective reaction than another route.

Carriers may also be used and are determined in part by the particularcomposition being administered, as well as by the particular method usedto administer the composition. Accordingly, there is a wide variety ofsuitable formulations of carriers that are available.

EXAMPLES Example 1 Characterization of AHAS Genomic Target SequencesIdentification of AHAS Sequences

The transcribed regions for three homoeologous AHAS genes wereidentified and determined. These novel sequences are listed as SEQ IDNO:1, SEQ ID NO:2, and SEQ ID NO:3. Previous sequencing effortsidentified and genetically mapped homoeologous copies of AHAS genes fromTriticum aestivum to the long arms of chromosomes 6A, 6B and 6D(Anderson et al., (2004) Weed Science 52:83-90; and, Li et al., (2008)Molecular Breeding 22:217-225). Sequence analysis of Expressed SequenceTags (EST) and genomic sequences available in Genbank (AccessionNumbers: AY210405.1, AY210407.1, AY210406.1, AY210408.1, FJ997628.1,FJ997629.1, FJ997631.1, FJ997630.1, FJ997627.1, AY273827.1) were used todetermine the transcribed region for the homoeologous copies of the AHASgene (SEQ ID NOs: 1-3).

The novel, non-coding sequences located upstream and downstream of thetranscribed region were characterized for the first time. To completelycharacterize theses non-coding sequences, the transcribed sequences foreach of the three homoeologous copies of the AHAS gene were used asBLASTN™ queries to screen unassembled ROCHE 454™ sequence reads that hadbeen generated from whole genome shotgun sequencing of Triticum aestivumcv. Chinese Spring. The ROCHE 454™ sequence reads of Triticum aestivumcv. Chinese Spring had been generated to 5-fold sequence coverage.Sequence assembly was completed using the SEQUENCHER SOFTWARE™(GeneCodes, Ann Arbor, Mich.) of the ROCHE 454™ Sequence reads with asignificant BLASTN™ hit (E-value <0.0001) were used to characterizethese non-transcribed region. Iterative rounds of BLASTN™ analysis andsequence assembly were performed. Each iteration incorporated theassembled AHAS sequence from the previous iteration so that all of thesequences were compiled as a single contiguous sequence. Overall, 4,384,7,590 and 6,205 of genomic sequences for the homoeologous AHAS geneslocated on chromosomes 6A, 6B and 6D, respectively, were characterized(SEQ ID NOs:4-6).

Sequence Analysis of AHAS Genes Isolated from Triticum aestivum Cv.Bobwhite MPB26RH

The homoeologous copies of the AHAS gene were cloned and sequenced fromTriticum aestivum cv. Bobwhite MPB26RH to obtain nucleotide sequencesuitable for designing specific zinc finger proteins that could bind thesequences with a high degree of specificity. The sequence analysis ofthe AHAS nucleotide sequences obtained from Triticum aestivum cv.Bobwhite MPB26RH was required to confirm the annotation of nucleotidespresent in Genbank and ROCHE 454™ AHAS gene sequences and due to allelicvariation between cv. Bobwhite MPB26RH and the other wheat varietiesfrom which the Genbank and ROCHE 454™ sequences were obtained.

A cohort of PCR primers (Table 1) were designed for amplification of theAHAS genes. The primers were designed from a consensus sequence whichwas produced from multiple sequence alignments generated using CLUSTALW™(Thompson et al., (1994) Nucleic Acids Research 22:4673-80). Thesequence alignments were assembled from the cv. Chinese Springsequencing data generated from ROCHE 454™ sequencing which was completedat a 5-fold coverage.

As indicated in Table 1, the PCR primers were designed to amplify allthree homoeologous sequences or to amplify only a single homoeologoussequence. For example, the PCR primers used to amplify the transcribedregion of the AHAS gene were designed to simultaneously amplify allthree homoeologous copies in a single multiplex PCR reaction. The PCRprimers used to amplify the non-transcribed region were either designedto amplify all three homoeologous copies or to amplify only a singlehomoeologous copy. All of the PCR primers were designed to be between 18and 27 nucleotides in length and to have a melting temperature of 60 to65° C., optimal 63° C. In addition, several primers were designed toposition the penultimate base (which contained a phosphorothioatelinkage and is indicated in Table 1 as an asterisk [*]) over anucleotide sequence variation that distinguished the gene copies fromeach wheat sub-genome. Table 1 lists the PCR primers that were designedand synthesized.

TABLE 1  Primer sequences used for PCR amplification of AHAS sequencesGenome SEQ ID Primer Name Region Amplified NO. Sequence (5′→3′)AHAS-p_Fwd5 5′ UTR D 7 TCTGTAAGTTATCGCCT GAATTGCTT AHAS-p_Rvs6 5′ UTR D8 CATTGTGACATCAGCA TGACACAA AHAS-p_Fwd4 5′ UTR D 9 AAGCAYGGCTTGCCTA CAGCAHAS-p_Rvs3 5′ UTR D 10 AACCAAATRCCCCTAT GTCTCTCC AHAS-p_Fwd1 5′ UTRA, B, and 11 CGTTCGCCCGTAGACC D ATTC AHAS-p_Rvs1 5′ UTR A, B, and 12GGAGGGGTGATGKTTT D TGTCTTT AHAS_1F1_ Coding A, B, and 13TCG CCC AAA CCC TCG transcribed D CC AHAS_1R1_ Coding A, B, and 14GGG TCG TCR CTG GGG transcribed D AAG TT AHAS_2F2_ Coding A, B, and 15GCC TTC TTC CTY GCR transcribed D TCC TCT GG AHAS_2R2_ Coding A, B, and16 GCC CGR TTG GCC TTG transcribed D TAA AAC CT AHAS_3F1_ CodingA, B, and 17 AYC AGA TGT GGG transcribed D CGG CTC AGT AT AHAS_3R1_Coding A, B, and 18 GGG ATA TGT AGG transcribed D ACA AGA AAC TTG CAT GAAHAS- 3′UTR A 19 AGGGCCATACTTGTTG 6A.PS.3′.F1 GATATCAT*C AHAS- 3′UTR A20 GCCAACACCCTACACT 6A.PS.3′.R2 GCCTA*T AHAS- 3′UTR B 21TGCGCAATCAGCATGA 6B.PS.3′.F1 TACC*T AHAS- 3′UTR B 22 ACGTATCCGCAGTCGA6B.PS.3′.R1 GCAA*T AHAS- 3′UTR D 23 GTAGGGATGTGCTGTC 6D.PS.3′.F1ATAAGAT*G AHAS- 3′UTR D 24 TTGGAGGCTCAGCCGA 6D.PS.3′.R3 TCA*C UTR =untranslated region Coding = primers designed for the transcribedregions asterisk (*) indicates the incorporation of a phosphorothioatesequence

Sub-genome-specific amplification was achieved using on-off PCR (Yang etal., (2005) Biochemical and Biophysical Research Communications328:265-72) with primers that were designed to position the penultimatebase (which contained a phosphorothioate linkage) over a nucleotidesequence variation that distinguished the gene copies from each wheatsub-genome. Two different sets of PCR conditions were used to amplifythe homoeologous copies of the AHAS gene from cv. Bobwhite MPB26RH. Forthe transcribed regions, the PCR reaction contained 0.2 mM dNTPs, 1×IMMOLASE PCR™ buffer (Bioline, Taunton, Mass.), 1.5 mM MgCl₂, 0.25 unitsIMMOLASE DNA POLYMERASE™ (Bioline, Taunton, Mass.), 0.2 μM each offorward and reverse primer, and about 50 ng genomic DNA. Reactionscontaining the AHAS_(—)1F1 and AHAS_(—)1R1 primers were supplementedwith 8% (v/v) DMSO. For the non-transcribed regions, the PCR reactionscontained 0.2 mM dNTP, 1× PHUSION GC BUFFER™ (New England BiolabsIpswich, MA), 0.5 units HOT-START PHUSION DNA™ polymerase (New EnglandBiolabs), 0.2 μM each of forward and reverse primer, and about 50 nggenomic DNA. PCR was performed in a final 25 μl reaction volume using anMJ PTC200® thermocycler (BioRad, Hercules, Calif.). Following PCRcycling, the reaction products were purified and cloned using PGEM-TEASY VECTOR™ (Promega, Madison, Wis.) into E. coli JM10⁹ cells. PlasmidDNA was extracted using a DNAEASY PLASMID DNA PURIFICATION KIT™ (Qiagen,Valencia, Calif.) and Sanger sequenced using BIGDYE® v3.1 chemistry(Applied Biosystems, Carlsbad, Calif.) on an ABI3730XL® automatedcapillary electrophoresis platform. Sequence analysis performed usingSEQUENCHER SOFTWARE™ (GeneCodes, Ann Arbor, Mich.) was used to generatea consensus sequence for each homoeologous gene copy (SEQ ID NO:25, SEQID NO:26, and SEQ ID NO:27) from cv. Bobwhite MPB26RH. CLUSTALW™ wasused to produce a multiple consensus sequence alignment from whichhomoeologous sequence variation distinguishing between the AHAS genecopies was confirmed.

Example 2 Design of Zinc Finger Binding Domains Specific to AHAS GeneSequences

Zinc finger proteins directed against the identified DNA sequences ofthe homoeologous copies of the AHAS genes were designed as previouslydescribed. See, e.g., Urnov et al., (2005) Nature 435:646-551. Exemplarytarget sequence and recognition helices are shown in Table 2(recognition helix regions designs) and Table 3 (target sites). In Table3, nucleotides in the target site that are contacted by the ZFPrecognition helices are indicated in uppercase letters; non-contactednucleotides are indicated in lowercase. Zinc Finger Nuclease (ZFN)target sites were in 4 regions in the AHAS gene: a region about 500-bpupstream of the serine 653 amino acid residue, an upstream regionadjacent (within 30-bp) to the serine 653 amino acid residue, adownstream region adjacent (within 80-bp) to the serine 653 amino acidresidue, and a region about 400-bp downstream of the serine 653 aminoacid residue.

TABLE 2  AHAS zinc finger designs (N/A indicates “not applicable”) ZFP #F1 F2 F3 F4 F5 F6 29964 QSSHLTR RSDDLTR RSDDLTR YRWLLRS QSGDLTR QRNARTLSEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 181  NO: 182  NO: 182 NO: 183  NO: 184  NO: 185 29965 RSDNLSV QKINLQV DDWNLSQ RSANLTR QSGHLARNDWDRRV SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 186  NO: 187 NO: 188  NO: 189  NO: 190  NO: 191 29966 RSDDLTR YRWLLRS_ QSGDLTRQRNARTL_ RSDHLSQ_ DSSTRKK SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ IDNO: 182  NO: 183  NO: 184  NO: 185  NO: 192  NO: 193 29967 RSDDLTRYRWLLRS_ QSGDLTR QRNARTL RSDVLSE DRSNRIK SEQ ID SEQ ID SEQ ID SEQ IDSEQ ID SEQ ID NO: 182  NO: 183  NO: 184  NO: 185  NO: 194  NO: 195 29968RSDNLSN TSSSRIN DRSNLTR QSSDLSR QSAHRKN N/A SEQ ID SEQ ID SEQ ID SEQ IDSEQ ID NO: 196  NO: 197  NO: 198  NO: 199  NO: 200 29969 DRSHLTR QSGHLSRRSDNLSV QKINLQV DDWNLSQ RSANLTR SEQ ID SEQ ID SEQ ID SEQ ID SEQ IDSEQ ID NO: 201  NO: 202  NO: 186  NO: 187  NO: 188  NO: 189 29970QSGDLTR QRNARTL RSDVLSE DRSNRIK RSDNLSE HSNARKT SEQ ID SEQ ID SEQ IDSEQ ID SEQ ID SEQ ID NO: 184  NO: 185  NO: 194  NO: 195  NO: 203 NO: 204 29971 DRSHLTR QSGHLSR RSDNLSN TSSSRIN DRSNLTR N/A SEQ ID SEQ IDSEQ ID SEQ ID SEQ ID NO: 201  NO: 202  NO: 196  NO: 197  NO: 198 29730TSGNLTR HRTSLTD QSSDLSR HKYHLRS QSSDLSR QWSTRKR SEQ ID SEQ ID SEQ IDSEQ ID SEQ ID SEQ ID NO: 205  NO: 206  NO: 199  NO: 207  NO: 199 NO: 208 29731 RSDVLSE SPSSRRT RSDTLSE TARQRNR DRSHLAR N/A SEQ ID SEQ IDSEQ ID SEQ ID SEQ ID NO: 194  NO: 209  NO: 210  NO: 211  NO: 212 29732RSDSLSA_ RSDALAR_ RSDDLTR_ QKSNLSS_ DSSDRKK_ N/A SEQ ID SEQ ID SEQ IDSEQ ID SEQ ID NO: 213  NO: 214  NO: 182  NO: 215  NO: 216 30006 TSGNLTR_WWTSRAL_ DRSDLSR_ RSDHLSE_ YSWRLSQ_ N/A SEQ ID SEQ ID SEQ ID SEQ IDSEQ ID NO: 205  NO: 217  NO: 218  NO: 219  NO: 220 30008 RSDSLSV_RNQDRKN_ QSSDLSR HKYHLRS_ QSGDLTR_ N/A SEQ ID SEQ ID SEQ ID  SEQ IDSEQ ID NO: 221  NO: 222  NO: 199  NO: 207  NO: 184 29753 QSGNLAR_DRSALAR_ RSDNLST AQWGRTS_ N/A N/A SEQ ID SEQ ID SEQ ID SEQ ID NO: 223 NO: 224  NO: 225  NO: 226 29754 RSADLTR_ TNQNRIT_ RSDSLLR_ LQHHLTD_QNATRIN_ N/A SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 227  NO: 228 NO: 229  NO: 230  NO: 231 29769 QSGNLAR_ DRSALAR_ RSDNLST_ AQWGRTS_ N/AN/A SEQ ID SEQ ID SEQ ID SEQ ID NO: 223  NO: 224  NO: 225  NO: 226 29770QSGDLTR MRNRLNR_ DRSNLSR_ WRSCRSA RSDNLSV_ N/A SEQ ID SEQ ID SEQ IDSEQ ID SEQ ID NO: 184  NO: 232  NO: 233  NO: 234  NO: 186 30012 HSNARKTQSGNLAR DRSALAR RSDNLST AQWGRTS_ N/A SEQ ID SEQ ID SEQ ID SEQ ID SEQ IDNO: 204  NO: 223  NO: 224  NO: 225  NO: 226 30014 HSNARKT QSGNLARDRSALAR RSDHLSQ QWFGRKN_ N/A SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 204 NO: 223  NO: 224  NO: 192  NO: 235 30018 QSGDLTR MRNRLNR DRSNLSR WRSCRSAQRSNLDS_ N/A SEQ ID     SEQ ID SEQ ID SEQ ID SEQ ID NO: 184  NO: 232 NO: 233  NO: 234  NO: 34 29988 QSGDLTR QWGTRYR DRSNLSR HNSSLKD QSGNLAR_N/A SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 184  NO: 33 NO: 233  NO: 32NO: 223 29989 RSDVLSA RNDHRIN RSDHLSQ QSAHRTN DRSNLSR_ DSTNRYR_ SEQ IDSEQ ID SEQ ID  SEQ ID  SEQ ID SEQ ID NO: 31 NO: 30 NO: 192  NO: 29NO: 233 NO: 28

TABLE 3  Target site of AHAS zinc fingers SEQ ID ZFP AHAS RegionTarget Site (5′→3′) NO: 29964 500-bp upstream ofggATAGCAtATTGCGGCGGGAtggcctc 35 5653 29965 500-bp upstream ofgtACTGGAtGAGCTGaCAAAAGgggagg 36 S653 29966 500-bp upstream ofgtACCTGGATAGCAtATTGCGgcgggat 37 S653 29967 500-bp upstream ofagTACCTGgATAGCAtATTGCGgcggga 38 S653 29968 500-bp upstream ofgaTGAGCTGACAAAAGGggaggcgatca 39 S653 29969 500-bp upstream ofatGAGCTGaCAAAAGgGGAGGCgatcat 40 S653 29970 500-bp upstream oftcATCCAGTACCTGgATAGCAtattgcg 41 S653 29971 500-bp upstream ofctGACAAAAGGGGAGGCgatcattgcca 42 S653 29730 Within 30-bpagGCAGCACGTGCTCCTGATgcgggact 43 upstream of S653 29731 Within 30-bptaGGCAGCACGtgCTCCTGatgcgggac 44 upstream of S653 29732 Within 30-bpgaTCCCAAGCGGTGGTGctttcaaggac 45 upstream of S653 30006 Within 30-bptgATGCGGGACTATGATatccaacaagt 46 upstream S653 30008 Within 30-bpgaGCACGTGCTgCCTATGatcccaagcg 47 upstream S653 29753 Within 80-bptcTTGTAGGTCGAAatttcagtacgagg 48 downstream of S653N 29754 Within 80-bpctACAAGTGTGaCATGCGcaatcagcat 49 downstream of S653N 29769 Within 80-bpcTTGTAGGTCGAAa 50 downstream of S653N 29770 Within 80-bpcAAGTGTGACaTGCGCAa 51 downstream of S653N 30012 Within 80-bptcTTGTAGGTCGAAATTtcagtacgagg 52 downstream of S653N 30014 Within 80-bptcTTGTAGGTCGAAATTtcagtacgagg 53 downstream of S653N 30018 Within 80-bptaCAAgTGTGACaTGCGCAatcagcatg 54 downstream of S653N 29988400-bp downstream caGAACCTGACACAGCAgacatgtaaag 55 of S653 29989400-bp downstream atAACGACCGATGGAGGGTGgtcggcag 56 of S653

The AHAS zinc finger designs were incorporated into zinc fingerexpression vectors encoding a protein having at least one finger with aCCHC structure. See, U.S. Patent Publication No. 2008/0182332. Inparticular, the last finger in each protein had a CCHC backbone for therecognition helix. The non-canonical zinc finger-encoding sequences werefused to the nuclease domain of the type IIS restriction enzyme FokI(amino acids 384-579 of the sequence of Wah et al., (1998) Proc. Natl.Acad. Sci. USA 95:10564-10569) via a four amino acid ZC linker and anopaque-2 nuclear localization signal derived from Zea mays to form AHASzinc-finger nucleases (ZFNs). See, U.S. Pat. No. 7,888,121.

The optimal zinc fingers were verified for cleavage activity using abudding yeast based system previously shown to identify activenucleases. See, e.g., U.S. Patent Publication No. 2009/0111119; Doyon etal., (2008) Nat Biotechnology 26:702-708; Geurts et al., (2009) Science325:433. Zinc fingers for the various functional domains were selectedfor in vivo use. Of the numerous ZFNs that were designed, produced andtested to bind to the putative AHAS genomic polynucleotide target sites,13 ZFNs were identified as having in vivo activity at high levels, andselected for further experimentation. Eleven of the ZFNs were designedto bind to the three homoeologous gene copies and two ZFNs(29989-2A-29988 and 30006-2A-30008) were designed to only bind the genecopy on chromosome 6D. The 13 ZFNs were characterized as being capableof efficiently binding and cleaving the unique AHAS genomicpolynucleotide target sites in planta. Exemplary vectors are describedbelow.

Example 3 Evaluation of Zinc Finger Nuclease Cleavage of AHAS GenesUsing Transient Assays ZFN Construct Assembly

Plasmid vectors containing ZFN gene expression constructs, which wereidentified using the yeast assay as described in Example 2, weredesigned and completed using skills and techniques commonly known in theart. Each ZFN-encoding sequence was fused to a sequence encoding anopaque-2 nuclear localization signal (Maddaloni et al., (1989) Nuc.Acids Res. 17:7532), that was positioned upstream of the zinc fingernuclease.

Expression of the fusion proteins was driven by the constitutivepromoter from the Zea mays Ubiquitin gene which includes the 5′untranslated region (UTR) (Toki et al., (1992) Plant Physiology 100;1503-07). The expression cassette also included the 3′ UTR (comprisingthe transcriptional terminator and polyadenylation site) from the Zeamays peroxidase (Per5) gene (US Patent Publication No. 2004/0158887).The self-hydrolyzing 2A encoding the nucleotide sequence from Thoseaasigna virus (Szymczak et al., (2004) Nat Biotechnol. 22:760-760) wasadded between the two Zinc Finger Nuclease fusion proteins that werecloned into the construct.

The plasmid vectors were assembled using the IN-FUSION™ AdvantageTechnology (Clontech, Mountain View, Calif.). Restriction endonucleaseswere obtained from New England BioLabs (Ipswich, MA) and T4 DNA Ligase(Invitrogen, Carlsbad, Calif.) was used for DNA ligation. Plasmidpreparations were performed using NUCLEOSPIN® Plasmid Kit(Macherey-Nagel Inc., Bethlehem, Pa.) or the Plasmid Midi Kit (Qiagen)following the instructions of the suppliers. DNA fragments were isolatedusing QIAQUICK GEL EXTRACTION KIT™ (Qiagen) after agarose tris-acetategel electrophoresis. Colonies of ligation reactions were initiallyscreened by restriction digestion of miniprep DNA. Plasmid DNA ofselected clones was sequenced by a commercial sequencing vendor(Eurofins MWG Operon, Huntsville, Ala.). Sequence data were assembledand analyzed using the SEQUENCHER™ software (Gene Codes Corp., AnnArbor, Mich.).

The resulting 13 plasmid constructs: pDAB109350 (ZFNs 29732-2A-29730),pDAB109351 (ZFNs 29732-2A-29731), pDAB109352 (ZFNs 29753-2A-29754),pDAB109353 (ZFNs 29968-2A-29967), pDAB109354 (ZFNs 29965-2A-29964),pDAB109355 (ZFNs 29968-2A-29966), pDAB109356 (ZFNs 29969-2A-29967),pDAB109357 (ZFNs 29971-2A-29970), pDAB109358 (ZFNs 29989-2A-29988),pDAB109359 (ZFNs 30006-2A-30008), pDAB109360 (ZFNs 30012-2A-30018),pDAB109361 (ZFNs 30014-2A-30018) and pDAB109385 (ZFNs 29770-2A-29769)were confirmed via restriction enzyme digestion and via DNA sequencing.

Representative plasmids pDAB109350 and pDAB109360 are shown in FIG. 1and FIG. 2.

Preparation of DNA from ZFN Constructs for Transfection

Before delivery to Triticum aestivum protoplasts, plasmid DNA for eachZFN construct was prepared from cultures of E. coli using the PURE YIELDPLASMID MAXIPREP SYSTEM® (Promega Corporation, Madison, Wis.) or PLASMIDMAXI KIT® (Qiagen, Valencia, Calif.) following the instructions of thesuppliers.

Isolation of Wheat Mesophyll Protoplasts

Mesophyll protoplasts from the wheat line cv. Bobwhite MPB26RH wereprepared for transfection using polyethylene glycol (PEG)-mediated DNAdelivery as follows.

Mature seed was surface sterilized by immersing in 80% (v/v) ethanol for30 secs, rinsing twice with tap water, followed by washing in 20%DOMESTOS® (0.8% v/v available chlorine) on a gyratory shaker at 140 rpmfor 20 mins. The DOMESTOS® was removed by decanting and the seeds wererinsed four times with sterile water. Excess water was removed byplacing the seed on WHATMAN™ filter paper. The seeds were placed in asterile PETRI™ dish on several sheets of dampened sterile WHATMAN™filter paper and incubated for 24 h at 24° C. Following incubation, theseeds were surface sterilized a second time in 15% DOMESTOS® with 15 minshaking, followed by rinsing with sterile water as described previously.The seeds were placed on Murashige and Skooge (MS) solidified media for24 hr at 24° C. Finally, the seeds were surface sterilized a third timein 10% DOMESTOS® with 10 min shaking, followed by rinsing in sterilewater as previously described. The seeds were placed, crease side down,onto MS solidified media with 10 seeds per PETRI™ dish and germinated inthe dark at 24° C. for 14-21 days.

About 2-3 grams of leaf material from the germinated seeds was cut into2-3 cm lengths and placed in a pre-weighed PETRI™ dish. Leaf sheath andyellowing leaf material was discarded. Approximately 10 mL of leafenzyme digest mix (0.6 M mannitol, 10 mM MES, 1.5% w/v cellulase R10,0.3% w/v macerozyme, 1 mM CaCl₂, 0.1% bovine serum albumin, 0.025% v/vpluronic acid, 5 mM β-mercaptoethanol, pH 5.7) was pipetted into thePETRI™ dish and the leaf material was chopped transversely into 1-2 mmsegments using a sharp scalpel blade. The leaf material was chopped inthe presence of the leaf digest mix to prevent cell damage resultingfrom the leaf material drying out. Additional leaf enzyme digest mix wasadded to the PETRI™ dish to a volume of 10 mL per gram fresh weight ofleaf material and subject to vacuum (20″ Hg) pressure for 30 min. ThePETRI™ dish was sealed with PARAFILM® and incubated at 28° C. withgentle rotational shaking for 4-5 hours.

Mesophyll protoplasts released from the leaf segments into the enzymedigest mix were isolated from the plant debris by passing the digestionsuspension through a 100 micron mesh and into a 50 mL collection tube.To maximize the yield of protoplasts, the digested leaf material waswashed three times. Each wash was performed by adding 10 mL wash buffer(20 mM KCl, 4 mM MES, 0.6 M mannitol, pH 5.6) to the PETRI™ dish,swirling gently for 1 min, followed by passing of the wash bufferthrough the 100 micron sieve into the same 50 mL collection tube. Next,the filtered protoplast suspension was passed through a 70 micron sieve,followed by a 40 micron sieve. Next, 6 mL aliquots of the filteredprotoplast suspension were transferred to 12 mL round bottomedcentrifugation tubes with lids and centrifuged at 70 g and 12° C. for 10min. Following centrifugation, the supernatant was removed and theprotoplast pellets were each resuspended in 7 mL wash buffer. Theprotoplasts were pelleted a second time by centrifugation, as describedabove. The protoplasts were each resuspended in 1 mL wash buffer andpooled to two centrifugation tubes. The wash buffer volume was adjustedto a final volume of 7 mL in each tube before centrifugation wasperformed, as described above. Following removal of the supernatant, theprotoplast pellets were resuspended in 1 mL wash buffer and pooled to asingle tube. The yield of mesophyll protoplasts was estimated using aNeubauer haemocytometer. Evans Blue stain was used to determine theproportion of live cells recovered.

PEG-Mediated Transfection of Mesophyll Protoplasts

About 10⁶ mesophyll protoplasts were added to a 12 mL round bottomedtube and pelleted by centrifugation at 70 g before removing thesupernatant. The protoplasts were gently resuspended in 600 μl washbuffer containing 70 μg of plasmid DNA. The plasmid DNA consisted of theZinc Finger Nuclease constructs described above. Next, an equal volumeof 40% PEG solution (40% w/v PEG 4,000, 0.8 M mannitol, 1M Ca(NO₃)₂, pH5.6) was slowly added to the protoplast suspension with simultaneousmixing by gentle rotation of the tube. The protoplast suspension wasallowed to incubate for 15 min at room temperature without anyagitation.

An additional 6 mL volume of wash buffer was slowly added to theprotoplast suspension in sequential aliquots of 1 mL, 2 mL and 3 mL.Simultaneous gentle mixing was used to maintain a homogenous suspensionwith each sequential aliquot. Half of the protoplast suspension wastransferred to a second 12 mL round bottomed tube and an additional 3 mLvolume of wash buffer was slowly added to each tube with simultaneousgentle mixing. The protoplasts were pelleted by centrifugation at 70 gfor 10 min and the supernatant was removed. The protoplast pellets wereeach resuspended in 1 mL wash buffer before protoplasts from the pairedround bottomed tubes were pooled to a single 12 mL tube. An additional 7mL wash buffer was added to the pooled protoplasts before centrifugationas described above. The supernatant was completely removed and theprotoplast pellet was resuspended in 2 mL Qiao's media (0.44% w/v MSplus vitamins, 3 mM MES, 0.0001% w/v 2,4-D, 0.6 M glucose, pH 5.7). Theprotoplast suspension was transferred to a sterile 3 cm PETRI™ dish andincubated in the dark for 24° C. for 72 h.

Genomic DNA Isolation from Mesophyll Protoplasts

Transfected protoplasts were transferred from the 3 cm PETRI™ dish to a2 mL microfuge tube. The cells were pelleted by centrifugation at 70 gand the supernatant was removed. To maximize the recovery of transfectedprotoplasts, the PETRI™ dish was rinsed three times with 1 mL of washbuffer. Each rinse was performed by swirling the wash buffer in thePETRI™ dish for 1 min, followed by transfer of the liquid to the same 2ml microfuge tube. At the end of each rinse, the cells were pelleted bycentrifugation at 70 g and the supernatant was removed. The pelletedprotoplasts were snap frozen in liquid nitrogen before freeze drying for24 h in a LABCONCO FREEZONE 4.5® (Labconco, Kansas City, Mo.) at −40° C.and 133×10⁻³ mBar pressure. The lyophilized cells were subjected to DNAextraction using the DNEASY® PLANT DNA EXTRACTION MINI kit (Qiagen)following the manufacturer's instructions, with the exception thattissue disruption was not required and the protoplast cells were addeddirectly to the lysis buffer.

PCR Assay of Protoplast Genomic DNA for ZFN Sequence Cleavage

To enable the cleavage efficacy and target site specificity of ZFNsdesigned for the AHAS gene locus to be investigated, PCR primers weredesigned to amplify up to a 300-bp fragment within which one or more ZFNtarget sites were captured. One of the primers was designed to be withina 100-bp window of the captured ZFN target site(s). This design strategyenabled Illumina short read technology to be used to assess theintegrity of the target ZFN site in the transfected protoplasts. Inaddition, the PCR primers were designed to amplify the threehomoeologous copies of the AHAS gene and to capture nucleotide sequencevariation that differentiated between the homoeologs such that theIllumina sequence reads could be unequivocally attributed to the wheatsub-genome from which they were derived.

A total of four sets of PCR primers were designed to amplify the ZFNtarget site loci (Table 4). Each primer set was synthesized with theIllumina SP1 and SP2 sequences at the 5′ end of the forward and reverseprimer, respectively, to provide compatibility with Illumina short readsequencing chemistry. The synthesized primers also contained aphosphorothioate linkage at the penultimate 5′ and 3′ nucleotides(indicated in Table 4 as an asterisk [*]). The 5′ phosphorothioatelinkage afforded protection against exonuclease degradation of theIllumina SP1 and SP2 sequences, while the 3′ phosphorothioate linkageimproved PCR specificity for amplification of the target AHAS sequencesusing on-off PCR (Yang et al., (2005)). All PCR primers were designed tobe between 18 and 27 nucleotides in length and to have a meltingtemperature of 60 to 65° C., optimal 63° C.

In Table 4, nucleotides specific for the AHAS gene are indicated inuppercase type; nucleotides corresponding to the Illumina SP1 and SP2sequences are indicated in lowercase type. Each primer set wasempirically tested for amplification of the three homoeologous AHAS genecopies through Sanger-based sequencing of the PCR amplificationproducts.

TABLE 4 Primer sequences used to assess AHAS ZFN cleavage efficacy and targetsite specificity Primer SEQ ID Name AHAS Region Primer Sequence (5′→3′)NO: AHAS−500ZFN.F3 500-bp upstream a*cactctttccctacacgacgctcttccgatctT57 of S653 CCTCTAGGATTCAAGACTTTTG*G AHAS−500ZFN.R1 500-bp upstreamg*tgactggagttcagacgtgtgctcttccgatct 58 of S653 CGTGGCCGCTTGTAAGTGTA*AAHASs653ZFN.F1 Within 30-bp a*cactctttccctacacgacgctcttccgatctG 59upstream of S653 AGACCCCAGGGCCATACTT*G AHASs653ZFN.R3 Within 30-bpg*tgactggagttcagacgtgtgctcttccgatct 60 upstream of S653CAAGCAAACTAGAAAACGCATG*G AHASs653ZFN.F5 Within 80-bpa*cactctttccctacacgacgctcttccgatctA 61 downstream ofTGGAGGGTGATGGCAGGA*C S653N AHASs653ZFN.R1 Within 80-bpg*tgactggagttcagacgtgtgctcttccgatct 62 downstream ofATGACAGCACATCCCTACAAAAG*A S653N AHAS+400ZFN.F1 400-bpa*cactctttccctacacgacgctcttccgatctA 63 downstream ofACAGTGTGCTGGTTCCTTTCT*G S653 AHAS+400ZFN.R3 400-bpg*tgactggagttcagacgtgtgctcttccgatct 64 downstream ofTYTYYCCTCCCAACTGTATTCAG*A S653 asterisk (*) is used to indicate aphosphorothioate

PCR amplification of ZFN target site loci from the genomic DNA extractedfrom transfected wheat mesophyll protoplasts was used to generate therequisite loci specific DNA molecules in the correct format forIllumina-based sequencing-by-synthesis technology. Each PCR assay wasoptimized to work on 200 ng starting DNA (about 12,500 cell equivalentsof the Triticum aestivum genome). Multiple reactions were performed pertransfected sample to ensure sufficient copies of the Triticum aestivumgenome were assayed for reliable assessment of ZFN efficiency and targetsite specificity. About sixteen PCR assays, equivalent to 200,000 copiesof the Triticum aestivum genome taken from individual protoplasts, wereperformed per transfected sample. A single PCR master-mix was preparedfor each transfected sample. To ensure optimal PCR amplification of theZFN target site (i.e. to prevent PCR reagents from becoming limiting andto ensure that PCR remained in the exponential amplification stage) aninitial assay was performed using a quantitative PCR method to determinethe optimal number of cycles to perform on the target tissue. Theinitial PCR was performed with the necessary negative control reactionson a MX3000P THERMOCYCLER™ (Stratagene). From the data output gatheredfrom the quantitative PCR instrument, the relative increase influorescence was plotted from cycle-to-cycle and the cycle number wasdetermined per assay that would deliver sufficient amplification, whilenot allowing the reaction to become reagent limited, in an attempt toreduce over-cycling and biased amplification of common molecules. Theunused master mix remained on ice until the quantitative PCR analysiswas concluded and the optimal cycle number determined. The remainingmaster mix was then aliquoted into the desired number of reaction tubes(about 16 per ZFN assay) and PCR amplification was performed for theoptimal cycle number. Following amplification, samples for the same ZFNtarget site were pooled together and 200 μl of pooled product per ZFNwas purified using a QIAQUICK MINIELUTE PCR PURIFICATION KIT™ (Qiagen)following the manufacturer's instructions.

To enable the sample to be sequenced using Illumina short readtechnology, an additional round of PCR was performed to introduce theIllumina P5 and P7 sequences onto the amplified DNA fragments, as wellas a sequence barcode index that could be used to unequivocallyattribute sequence reads to the sample from which they originated. Thiswas achieved using primers that were in part complementary to the SP1and SP2 sequences added in the first round of amplification, but alsocontained the sample index and P5 and P7 sequences. The optimal numberof PCR cycles required to add the additional sequences to the templatewithout over-amplifying common fragments was determined by quantitativePCR cycle analysis, as described above. Following amplification, thegenerated product was purified using AMPURE MAGNETIC BEADS®(Beckman-Coulter) with a DNA-to-bead ratio of 1:1.7. The purified DNAfragment were titrated for sequencing by Illumina short read technologyusing a PCR-based library quantification kit (KAPA) according themanufacturer's instructions. The samples were prepared for sequencingusing a cBot cluster generation kit (Illumina) and were sequenced on anILLUMINA GAII_(X)™ or HISEQ2000™ instrument (Illumina) to generate100-bp paired end sequence reads, according to the manufacturer'sinstructions.

Data Analysis for Detecting NHEJ at Target ZFN Sites

Following generation of Illumina short read sequence data for samplelibraries prepared for transfected mesophyll protoplasts, bioinformaticsanalysis was performed to identify deleted nucleotides at the target ZFNsites. Such deletions are known to be indicators of in planta ZFNactivity that result from non-homologous end joining (NHEJ) DNA repair.

To identify sequence reads with NHEJ deletions, the manufacturer'ssupplied scripts for processing sequence data generated on theHISEQ2000™ instrument (Illumina) was used to first computationallyassign the short sequence reads to the protoplast sample from which theyoriginated. Sample assignment was based on the barcode index sequencethat was introduced during library preparation, as described previously.Correct sample assignment was assured as the 6-bp barcode indexes usedto prepare the libraries were differentiated from each other by at leasta two-step sequence difference.

Following sample assignment, a quality filter was passed across allsequences. The quality filter was implemented in custom developed PERLscript. Sequence reads were excluded if there were more than threeambiguous bases, or if the median Phred score was less than 20, or ifthere were three or more consecutive bases with a Phred score less than20, or if the sequence read was shorter than 40 nucleotides in length.

Next, the quality trimmed sequences were attributed to the wheatsub-genome from which they originated. This was achieved using a secondcustom developed PERL script in which sub-genome assignment wasdetermined from the haplotype of the nucleotide sequence variants thatwere captured by the PCR primers used to amplify the three homoeologouscopies of the AHAS gene, as described above.

Finally, the frequency of NHEJ deletions at the ZFN cleavage site in thesub-genome-assigned sequence reads was determined for each sample usinga third custom developed PERL script and manual data manipulation inMicrosoft Excel 2010 (Microsoft Corporation). This was achieved bycounting the frequency of unique NHEJ deletions on each sub-genomewithin each sample.

Two approaches were used to assess the cleavage efficiency andspecificity of the ZFNs tested. Cleavage efficiency was expressed (inparts per million reads) as the proportion of sub-genome assignedsequences that contained a NHEJ deletion at the ZFN target site. Rankordering of the ZFNs by their observed cleavage efficiency was used toidentify ZFNs with the best cleavage activity for each of the fourtarget regions of the AHAS genes in a sub-genome-specific manner.

All of the ZFNs tested showed NHEJ deletion size distributionsconsistent with that expected for in planta ZFN activity. Cleavagespecificity was expressed as the ratio of cleavage efficiencies observedacross the three sub-genomes. The inclusion of biological replicates inthe data analyses did not substantially affect the rank order forcleavage activity and specificity of the ZFNs tested.

From these results, the ZFNs encoded on plasmid pDAB109350 (i.e. ZFN29732 and 29730) and pDAB109360 (i.e. ZFN 30012 and 30018) were selectedfor in planta targeting in subsequent experiments, given theircharacteristics of significant genomic DNA cleavage activity in each ofthe three wheat sub-genomes.

Example 4 Evaluation of Donor Designs for ZFN-Mediated AHAS Gene EditingUsing Transient Assays

To investigate ZFN-mediated genomic editing at the endogenous AHAS genelocus in wheat, a series of experiments were undertaken to assess theeffect of donor design on the efficiency of homologous recombination(HR)-directed and non-homologous end joining (NHEJ)-directed DNA repair.These experiments used transient assays to monitor the efficiency forZFN-mediated addition of the previously described S653N mutationconferring tolerance to imidazolinone class herbicides (Li et al.,(2008) Molecular Breeding 22:217-225) at the endogenous AHAS gene locusin wheat, or alternatively for ZFN-mediated introduction of an EcoRIrestriction endonuclease sequence site at the double strand DNA breakcreated in the endogenous AHAS genes by targeted ZFN cleavage.

Donor Designs for HR-Directed DNA Repair

Donor DNA designs were based on a plasmid DNA vector containing 750-bphomology arms (i.e. sequence identical to the endogenous AHAS gene)flanking each side of the target cleavage site for ZFNs 29732 and 29730.A plasmid DNA vector was designed for each of the three wheatsub-genomes: pDAS000132 (FIG. 3), pDAS000133 (FIG. 4) and pDAS000134(FIG. 5) were designed to the A-, B- and D-genome, respectively (SEQ IDNO:65, SEQ ID NO:66, and SEQ ID NO:67). Each plasmid DNA vector wasdesigned to introduce an S653N (AGC→ATT) mutation as a genomicmodification conferring tolerance to imidazolinone class herbicides atthe target homoeologous copy of the endogenous AHAS gene by ZFN-mediatedHR-directed DNA repair. Two additional plasmid DNA constructs were alsodesigned to target the D-genome. The first plasmid DNA, pDAS000135 (SEQID NO: 68) (FIG. 6), was identical to pDAS000134 except that itcontained two additional (synonymous) single nucleotide point mutations,one each located at 15-bp upstream and downstream of the S653N mutation.The second plasmid DNA, pDAS000131 (SEQ ID: 69) (FIG. 7), did notcontain the S653N mutation, but was designed to introduce an EcoRIrestriction endonuclease recognition site (i.e., GAATTC) at the doublestrand DNA break created by target ZFN cleavage in the D-genome copy ofthe endogenous AHAS gene.

Donor Designs for NHEJ-Directed DNA Repair

Two types of donor DNA designs were used for NHEJ-directed DNA repair.

The first type of donor design was a linear, double stranded DNAmolecule comprising 41-bp of sequence that shared no homology with theendogenous AHAS genes in wheat. Two donor DNA molecules were designed,each to target the three homoeologous copies of the AHAS gene. Bothdonor DNA molecules had protruding 5′ and 3′ ends to provide ligationoverhangs to facilitate ZFN-mediated NHEJ-directed DNA repair. The twodonor DNA molecules differed by the sequence at their protruding 3′ end.The first donor DNA molecule, pDAS000152 (SEQ ID NO:74 and SEQ IDNO:75), was designed to provide ligation overhangs that were compatiblewith those generated by cleavage of the endogenous AHAS genes by ZFNs29732 and 29730 (encoded on plasmid pDAB109350) and to result in theinsertion of the 41-bp donor molecule into the endogenous AHAS gene atthe site of the double strand DNA break via NHEJ-directed DNA repair.The second donor DNA molecule pDAS000149 (SEQ ID NO: 76 and SEQ IDNO:77) was designed to provide ligation overhangs that were compatiblewith those generated by the dual cleavage of the endogenous AHAS genesby ZFNs 29732 and 29730 (encoded on plasmid pDAB109350) and ZFNs 30012and 30018 (encoded on plasmid pDAB109360) and to result in thereplacement of the endogenous AHAS sequence contained between the twodouble strand DNA breaks created by the ZFNs with the 41-bp donormolecule via NHEJ-directed DNA repair.

The second type of donor was a plasmid DNA vector containing 41-bp ofsequence that shared no homology with the endogenous AHAS genes in wheatand that was flanked on either side by sequence that was recognized bythe ZFN(s) used to create double strand DNA breaks in the endogenousAHAS genes. This donor design allowed in planta release of the unique41-bp sequence from the plasmid DNA molecule by the same ZFN(s) used tocleave target sites in the endogenous AHAS genes, and simultaneousgeneration of protruding ends that were suitable for overhang ligationof the released 41-bp sequence into the endogenous AHAS genes viaNHEJ-directed DNA repair. Two plasmid donor DNA molecules were designed,each to target the three homoeologous copies of the AHAS gene. The firstplasmid donor molecule, pDAS000153 (SED ID NO:78 and SEQ ID NO:79) (FIG.8), was designed to provide ligation overhangs on the released 41-bp DNAfragment that were compatible with those generated by cleavage of theendogenous AHAS genes by ZFNs 29732 and 29730 (encoded on plasmidpDAB109350). The second plasmid donor molecule, pDAS000150 (SEQ ID NO:80and SEQ ID NO:81) (FIG. 9), was designed to provide ligation overhangson the released 41-bp DNA fragment that were at one end compatible withthose generated by ZFNs 29732 and 29730 (encoded on plasmid pDAB109350)and at the other end compatible with those generated by ZFNs 30012 and30018 (encoded on plasmid pDAB109360). This design allowed thereplacement of the endogenous AHAS sequence contained between the twodouble strand DNA breaks created by ZFNs 29732 and 29730 and ZFNs 30012and 30018 with the 41-bp donor molecule sequence.

Synthesis of Donor DNA for NHEJ-Directed and HDR-Directed DNA Repair

Standard cloning methods commonly known by one skilled in the art wereused to build the plasmid vectors. Before delivery to Triticum aestivum,plasmid DNA for each donor construct was prepared from cultures of E.coli using the PURE YIELD PLASMID MAXIPREP SYSTEM® (Promega Corporation,Madison, Wis.) or PLASMID MAXI KIT® (Qiagen, Valencia, Calif.) followingthe instructions of the suppliers.

Standard phosphoramidite chemistry was used to synthetically synthesizethe double stranded DNA donor molecules (Integrated DNA Technologies,Coralville, Iowa). For each donor molecule, a pair of complementarysingle stranded DNA oligomers was synthesized, each with twophosphorothioate linkages at their 5′ ends to provide protection againstin planta endonuclease degradation. The single stranded DNA oligomerswere purified by high performance liquid chromatography to enrich forfull-length molecules and purified of chemical carryover from thesynthesis steps using Na⁺ exchange. The double stranded donor moleculewas formed by annealing equimolar amounts of the two complementarysingle-stranded DNA oligomers using standard methods commonly known byone skilled in the art. Before delivery to Triticum aestivum, the doublestranded DNA molecules were diluted to the required concentration insterile water.

Isolation of Wheat Protoplasts Derived from Somatic Embryogenic Callus

Protoplasts derived from somatic embryogenic callus (SEC) from the donorwheat line cv. Bobwhite MPB26RH were prepared for transfection usingpolyethylene glycol (PEG)-mediated DNA delivery as follows:

Seedlings of the donor wheat line were grown in an environmentcontrolled growth room maintained at 18/16° C. (day/night) and a 16/8hour (day/night) photoperiod with lighting provided at 800 mmol m² persec. Wheat spikes were collected at 12-14 days post-anthesis and weresurface sterilized by soaking for 1 min in 70% (v/v) ethanol. The spikeswere threshed and the immature seeds were sterilized for 15 min in 17%(v/v) bleach with gentle shaking, followed by rinsing at least threetimes with sterile distilled water. The embryos were asepticallyisolated from the immature seeds under a dissecting microscope. Theembryonic axis was removed using a sharp scalpel and discarded. Thescutella were placed into a 9 cm PETRI™ dish containing 2-4 mediumwithout TIMENTIN™, with the uncut scutellum oriented upwards. A total of25 scutella were plated onto each 9 cm PETRI™ dish. Somatic embryogeniccallus (SEC) formation was initiated by incubating in the dark at 24° C.for 3 weeks. After 3 weeks, SEC was separated from non-embryogeniccallus, placed onto fresh 2-4 medium without TIMENTIN™ and incubated fora further 3 weeks in the dark at 24° C. Sub-culturing of SEC wasrepeated for a total of three times before being used for protoplastpreparation.

About one gram of SEC was chopped into 1-2 mm pieces using a sharpscalpel blade in a 10 cm PETRI™ dish contained approximately 10 mL ofwheat callus digest mix (2.5% w/v Cellulase RS, 0.2% w/v pectolyase Y23,0.1% w/v DRISELASE®, 14 mM CaCl₂, 0.8 mM MgSO₄, 0.7 mM KH₂PO₄, 0.6 MMannitol, pH 5.8) to prevent the callus from dehydrating. Additionalcallus digest mix was added to the PETRI™ dish to a volume of 10 mL pergram fresh weight of callus and subject to vacuum (20″ Hg) pressure for30 min. The PETRI™ dish was sealed with PARAFILM® and incubated at 28°C. with gentle rotational shaking at 30-40 rpm for 4-5 hours.

SEC protoplasts released from the callus were isolated by passing thedigestion suspension through a 100 micron mesh and into a 50 mLcollection tube. To maximize the yield of protoplasts, the digestedcallus material was washed three times. Each wash was performed byadding 10 mL SEC wash buffer (0.6 M Mannitol, 0.44% w/v MS, pH 5.8) tothe PETRI™ dish, swirling gently for 1 min, followed by passing of theSEC wash buffer through the 100 micron sieve into the same 50 mLcollection tube. Next, the filtered protoplast suspension was passedthrough a 70 micron sieve, followed by a 40 micron sieve. Next, 6 mLaliquots of the filtered protoplast suspension were transferred to 12 mLround bottomed centrifugation tubes with lids and centrifuged in at 70 gand 12° C. for 10 min. Following centrifugation, the supernatant wasremoved, leaving approximately 0.5 mL supernatant behind, and theprotoplast pellets were each resuspended in 7 mL of 22% sucrosesolution. The sucrose/protoplast mixture was carefully overlaid with 2mL SEC wash buffer, ensuring that there was no mixing of the twosolutions. The protoplasts were centrifuged a second time bycentrifugation, as described above. The band of protoplasts visiblebetween the SEC wash buffer and sucrose solution was collected using apipette and placed into a clean 12 mL round bottom tube. Seven mL of SECwash buffer was added to the protoplasts and the tubes were centrifuged,as described above. The supernatant was removed and the SEC protoplastswere combined to a single tube and resuspended in a final volume 1-2 mLof SEC wash buffer. The yield of SEC protoplasts was estimated using aNeubauer haemocytometer. Evans Blue stain was used to determine theproportion of live cells recovered.

PEG-Mediated Transfection of SEC Protoplasts

About two million SEC protoplasts were added to a 12 mL round bottomedtube and pelleted by centrifugation at 70 g before removing thesupernatant. The protoplasts were gently resuspended in 480 μl SEC washbuffer containing 70 μg of DNA. The DNA consisted of the Zinc FingerNuclease and donor DNA constructs described above, with each constructpresent at the molar ratio required for the experiment being undertaken.Next, 720 μl of 50% PEG solution (50% w/v PEG 4000, 0.8 M mannitol, 1MCa(NO₃)₂, pH 5.6) was slowly added to the protoplast suspension withsimultaneous mixing by gentle rotation of the tube. The protoplastsuspension was allowed to incubate for 15 min at room temperaturewithout any agitation.

An additional 7 mL volume of SEC wash buffer was slowly added to theprotoplast suspension in sequential aliquots of 1 mL, 2 mL and 3 mL.Simultaneous gentle mixing was used to maintain a homogenous suspensionwith each sequential aliquot. Half of the protoplast suspension wastransferred to a second 12 mL round bottomed tube and an additional 3 mLvolume of SEC wash buffer was slowly added to each tube withsimultaneous gentle mixing. The protoplasts were pelleted bycentrifugation at 70 g for 10 min and the supernatant was removed. Theprotoplast pellets were each resuspended in 1 mL SEC wash buffer beforeprotoplasts from the paired round bottomed tubes were pooled to a single12 mL tube. An additional 7 mL SEC wash buffer was added to the pooledprotoplasts before centrifugation as described above. The supernatantwas completely removed and the protoplast pellet was resuspended in 2 mLQiao's media. The protoplast suspension was transferred to a sterile 3cm PETRI™ dish and incubated in the dark for 24° C. for 72 h.

Isolation of Scutella from Immature Zygotic Wheat Embryos

Scutella of immature zygotic wheat embryos from the donor wheat line cv.Bobwhite MPB26RH were prepared for transfection usingbiolistics-mediated DNA delivery as follows.

Seedlings of the donor wheat line were grown in an environmentcontrolled growth room maintained at 18/16° C. (day/night) and a 16/8hour (day/night) photoperiod with lighting provided at 800 mmol m² persec. Wheat spikes were collected at 12-14 days post-anthesis and weresurface sterilized by soaking for 1 min in 70% (v/v) ethanol. The spikeswere threshed and the immature seeds were sterilized for 15 min in 17%(v/v) bleach with gentle shaking, followed by rinsing at least threetimes with sterile distilled water. The embryos were asepticallyisolated from the immature seeds under a dissecting microscope. Theembryonic axis was removed using a sharp scalpel and discarded. Thescutella were placed into a 9 cm PETRI™ dish containing osmotic MS (E3maltose) medium, with the uncut scutellum oriented upwards. A total of20 scutella were plated onto each 9 cm PETRI™ dish. The prepared embryoswere pre-cultured in the dark at 26° C. for a minimum of 4 h beforetransfection using biolistics-mediated DNA delivery.

Transfection of Scutella of Immature Zygotic Wheat Embryos byBiolistic-Mediated DNA Delivery

Gold particles for biolistic-mediated DNA delivery were prepared byadding 40 mg of 0.6 micron colloidal gold particles (BioRad) to 1 mL ofsterile water in a 1.5 mL microtube. The gold particles were resuspendedby vortexing for 5 min. To prepare sufficient material for 10bombardments, a 50 μL aliquot of the gold particle suspension wastransferred to a 1.5 mL microtube containing 5 μg of DNA resuspended in5 μL of sterile water. Following thorough mixing by vortexing, 50 μL of2.5 M CaCl₂ and 20 μL of 0.1 M spermidine were added to the microtube,with thorough mixing after the addition of each reagent. The DNA-coatedgold particles were pelleted by centrifugation for 1 min at maximumspeed in a bench top microfuge. The supernatant was removed and 1 mL of100% ethanol was added to wash and resuspend the gold particles. Thegold particles were pelleted by centrifugation, as described above, andthe supernatant discarded. The DNA-coated gold particles wereresuspended in 110 μL of 100% ethanol and maintained on ice. Following abrief vortex, 10 μL of the gold particle solution was placed centrallyonto a macro-carrier membrane and allowed to air dry.

The PDS-1000/HE PARTICLE GUN DELIVERY SYSTEM™ (BioRad) was used totransfect the scutella of immature zygotic wheat embryos bybiolistic-mediated DNA delivery. Delivery of the DNA-coated goldparticles was performed using the following settings: gap 2.5 cm,stopping plate aperture 0.8 cm, target distance 6.0 cm, vacuum 91.4-94.8kPa, vacuum flow rate 5.0 and vent flow rate 4.5. The scutella ofimmature zygotic wheat embryos were bombarded using a 900 psi rupturedisc. Each PETRI™ dish containing 20 scutella was bombarded once. Thebombarded scutella were incubated at 26° C. in the dark for 16 h beforebeing transferred onto medium for callus induction. The scutella werecultured on callus induction medium in the dark at 26° C. for 7 d.

Genomic DNA Isolation from SEC Protoplasts

Genomic DNA was extracted from SEC protoplasts using the procedurepreviously described for mesophyll protoplasts. An additionalpurification step was performed to reduce the presence of the donor DNAused for transfection. This was achieved using gel electrophoresis toseparate the genomic DNA from the SEC protoplasts from the donor DNAused for transfection. The extracted DNA was electrophoresed for 3 h ina 0.5% agarose gel using 0.5×TBE. The DNA was visualized by SYBR® SAFEstaining and the band corresponding to genomic DNA from the SECprotoplasts was excised. The genomic DNA was purified from the agarosegel using a QIAQUICK DNA PURIFICATION KIT™ (Qiagen), following themanufacturer's instructions, except that the QIAQUICK™ DNA purificationcolumn was replaced with a DNA binding column from the DNEASY PLANT DNAEXTRACTION MINI KIT™ (Qiagen).

Genomic DNA Isolation from Scutella of Immature Zygotic Embryos

The 20 scutella of immature zygotic wheat embryos transfected for eachbiolistic-mediated DNA delivery were transferred to a 15 ml tube andsnap frozen in liquid nitrogen before freeze drying for 24 h in aLABCONCO FREEZONE 4.5® (Labconco, Kansas City, Mo.) at −40° C. and133×10⁻³ mBar pressure. The lyophilized calli were subjected to DNAextraction using the DNEASY® PLANT DNA EXTRACTION MAXI™ KIT (Qiagen)following the manufacturer's instructions.

An additional purification step was performed to reduce the presence ofthe donor DNA used for transfection. This was achieved using gelelectrophoresis to separate the genomic DNA from the calli from thedonor DNA used for transfection. The extracted DNA was electrophoresedfor 3 h in a 0.5% agarose gel using 0.5×TBE. The DNA was visualized bySYBR® SAFE staining and the band corresponding to genomic DNA from thecalli was excised. The genomic DNA was purified from the agarose gelusing a QIAQUICK™ DNA PURIFICATION kit (Qiagen), following themanufacturer's instructions, except that the QIAQUICK™ DNA purificationcolumn was replaced with a DNA binding column from the DNEASY® PLANT DNAEXTRACTION MAXI™ KIT (Qiagen).

PCR Assay of Genomic DNA for ZEN-Mediated AHAS Editing

To investigate ZFN-mediated genomic editing at the endogenous AHAS genesin wheat using HR- and NHEJ-directed DNA repair, and assess the effectof donor DNA design on the efficacy of each DNA repair pathway, PCRassays were used to amplify the target AHAS regions from genomic DNA oftransfected wheat cells. PCR assays were performed as describedpreviously to generate requisite loci specific DNA molecules in thecorrect format for Illumina-based sequencing-by-synthesis technology.Each assay was performed using the previously described primer pair (SEQID NO: 59 and SEQ ID NO: 60) that were designed to amplify the regiontargeted by ZFNs 29732 and 29730 (encoded on plasmid pDAB109350) andZFNs 30012 and 30018 (encoded on plasmid pDAB109360) for each of thethree homoeologous copies of the AHAS genes. Multiple reactions wereperformed per transfected sample to ensure that sufficient copies of theTriticum aestivum genome were assayed for reliable assessment ofZFN-mediated gene editing. For transfected SEC protoplasts, up tosixteen PCR assays, equivalent to 200,000 copies of the Triticumaestivum genome taken from individual protoplasts, were performed pertransfected sample. For transfected scutella of immature zygoticembryos, about forty eight PCR assays, equivalent to 600,000 copies ofthe Triticum aestivum genome taken from individual protoplasts, wereperformed per transfected sample. Each transfected sample was preparedfor sequencing using a CBOT CLUSTER GENERATION KIT™ (Illumina) and wassequenced on an ILLUMINA GAII_(X)™ or HISEQ2000™ instrument (Illumina)to generate 100-bp paired end sequence reads, as described previously.

Data Analysis for Detecting ZFN-Mediated HR-Directed Editing at AHASGene Locus

Following generation of Illumina short read sequence data for samplelibraries prepared for transfected SEC protoplasts and scutella ofimmature zygotic wheat embryos, analyses were performed to identifymolecular evidence for ZFN-mediated HR-directed editing at the targetZFN sites.

To identify sequence reads with molecular evidence for HR-directed geneediting, the short sequence reads were first computationally processed,as previously described, to assign each read to the sample andsub-genome from which they originated, and to perform quality filteringto ensure that only high quality sequences were used for subsequentanalyses. Next, custom developed PERL scripts and manual datamanipulation in MICROSOFT EXCEL 2010™ (Microsoft Corporation) were usedto identify reads that contained sequence for both the donor DNAmolecule used for transfection and the endogenous AHAS locus. To ensureunequivocal discernment between sequence reads arising from ZFN-mediatedHR-directed gene editing and those resulting from the carryover of (any)donor DNA used for transfection, molecular evidence for gene editing wasdeclared only if the sequence read also contained a NHEJ deletion at theposition of the double strand DNA break created by the ZFN; i.e., thesequence read showed evidence for the outcome of imperfect HR-directedDNA repair. The editing frequency (expressed in parts per million reads)was calculated as the proportion of sub-genome-assigned sequence readsthat showed evidence for ZFN-mediated HR-directed gene editing.

From the results of three biological replicates performed for eachplasmid donor DNA design, molecular evidence was obtained for theenrichment of sequence reads showing ZFN-mediated HR-directed editing atthe three homoeologous copies of the endogenous AHAS genes in wheat(Table 5 and Table 6). Strong molecular evidence was obtained for theaddition of an EcoRI restriction endonuclease site at the position ofthe double strand DNA break created by ZFNs 29732 and 29730 in all threehomoeologous copies of the endogenous AHAS gene in both samples of SECprotoplasts and scutella of immature zygotic embryos that weretransfected with pDAB109350 and pDAS000131. The frequency ofZFN-mediated HR-directed gene editing was highest in the D-genome towhich the donor DNA molecule was targeted. Similarly, strong molecularevidence was obtained for the introduction of donor polynucleotidecontaining the S653N mutation in all three homoeologous copies of theendogenous AHAS genes in samples of scutella of immature zygotic embryosthat were transfected with pDAB109350 and either pDAS000132, pDAS000133or pDAS000134; strong molecular evidence was also observed for samplesof SEC protoplasts transfected with pDAB109350 and pDAS000134. Thefrequency of ZFN-mediated HR-directed gene editing was again highest inthe sub-genome for which the donor DNA was designed. Importantly, theediting frequency in samples of SEC protoplasts and scutella of immaturezygotic embryos transfected with pDAB109350 and pDAS000135 was lower(about 10-fold) than that observed for samples transfected withpDAB109350 and pDAS000134. This result was expected due to the penaltyimposed on the efficiency for HR-directed DNA repair by the presence ofthe flanking mutations in the pDAS00135 donor design.

TABLE 5 Average HR-directed editing frequency in parts per million (ppm)across three biological replicates of scutella transfected with plasmiddonor DNA designs. Donor- Editing Sub- to-ZFN Frequency in Editinggenome molar Wheat Sub- Frequency Donor targeted ZFN ratio Genome (ppm)pDAS000131 D n/a n/a A 0 pDAS000131 D 29732-2A- 5:1 A 251 29730pDAS000131 D 29732-2A- 10:1  A 46 29730 pDAS000131 D n/a n/a B 0pDAS000131 D 29732-2A- 5:1 B 106 29730 pDAS000131 D 29732-2A- 10:1  B 1929730 pDAS000131 D n/a n/a D 3 pDAS000131 D 29732-2A- 5:1 D 2,577 29730pDAS000131 D 29732-2A- 10:1  D 642 29730 pDAS000132 A n/a n/a A 5pDAS000132 A 29732-2A- 5:1 A 2,353 29730 pDAS000132 A 29732-2A- 10:1  A1,800 29730 pDAS000132 A n/a n/a B 0 pDAS000132 A 29732-2A- 5:1 B 4229730 pDAS000132 A 29732-2A- 10:1  B 30 29730 pDAS000132 A n/a n/a D 0pDAS000132 A 29732-2A- 5:1 D 110 29730 pDAS000132 A 29732-2A- 10:1  D 6129730 pDAS000133 B n/a n/a A 0 pDAS000133 B 29732-2A- 5:1 A 230 29730pDAS000133 B 29732-2A- 10:1  A 149 29730 pDAS000133 B n/a n/a B 8pDAS000133 B 29732-2A- 5:1 B 5,528 29730 pDAS000133 B 29732-2A- 10:1  B4,472 29730 pDAS000133 B n/a n/a D 0 pDAS000133 B 29732-2A- 5:1 D 029730 pDAS000133 B 29732-2A- 10:1  D 0 29730 pDAS000134 D n/a n/a A 2pDAS000134 D 29732-2A- 5:1 A 316 29730 pDAS000134 D 29732-2A- 10:1  A959 29730 pDAS000134 D n/a n/a B 1 pDAS000134 D 29732-2A- 5:1 B 11029730 pDAS000134 D 29732-2A- 10:1  B 318 29730 pDAS000134 D n/a n/a D 19pDAS000134 D 29732-2A- 5:1 D 4,662 29730 pDAS000134 D 29732-2A- 10:1  D9,043 29730 pDAS000135 D n/a n/a A 0 pDAS000135 D 29732-2A- 5:1 A 3829730 pDAS000135 D 29732-2A- 10:1  A 97 29730 pDAS000135 D n/a n/a B 0pDAS000135 D 29732-2A- 5:1 B 14 29730 pDAS000135 D 29732-2A- 10:1  B 3129730 pDAS000135 D n/a n/a D 1 pDAS000135 D 29732-2A- 5:1 D 541 29730pDAS000135 D 29732-2A- 10:1  D 1,191 29730 “na” indicates “notapplicable.”

TABLE 6 Average HR-directed editing frequency in parts per million (ppm)across three biological replicates of SEC protoplasts transfected withplasmid donor DNA designs. Donor- Editing Sub- to-ZFN Frequency inEditing genome molar Wheat Sub- Frequency Donor targeted ZFN ratioGenome (ppm ) pDAS000131 D n/a n/a A 0 pDAS000131 D 29732-2A- 7:1 A 5029730 pDAS000131 D n/a 7:1 B 0 pDAS000131 D 29732-2A- 7:1 B 0 29730pDAS000131 D n/a 7:1 D 4 pDAS000131 D 29732-2A- 7:1 D 212 29730pDAS000134 D n/a 7:1 A 0 pDAS000134 D 29732-2A- 7:1 A 0 29730 pDAS000134D n/a 7:1 B 0 pDAS000134 D 29732-2A- 7:1 B 0 29730 pDAS000134 D n/a 7:1D 32 pDAS000134 D 29732-2A- 7:1 D 258 29730 pDAS000135 D n/a 7:1 A 0pDAS000135 D 29732-2A- 7:1 A 0 29730 pDAS000135 D n/a 7:1 B 0 pDAS000135D 29732-2A- 7:1 B 0 29730 pDAS000135 D n/a 7:1 D 0 pDAS000135 D29732-2A- 7:1 D 1 29730 “na” indicates “not applicable.”

Data Analysis for Detecting ZFN-Mediated NHEJ-Directed Editing at AHASGenes

Following generation of Illumina short read sequence data for samplelibraries prepared for transfected SEC protoplasts and scutella ofimmature zygotic wheat embryos, analyses were performed to identifymolecular evidence for ZFN-mediated NHEJ-directed editing at the targetZFN sites.

To identify sequence reads with molecular evidence for NHEJ-directedgene editing, the short sequence reads were first computationallyprocessed, as previously described, to assign each read to the sampleand sub-genome from which they originated, and to perform qualityfiltering to ensure that only high quality sequences were used forsubsequent analyses. Next, custom developed PERL scripts and manual datamanipulation in Microsoft Excel 2010 (Microsoft Corporation) was used toidentify reads that contained sequence for both the donor DNA moleculeused for transfection and the endogenous AHAS locus. The editingfrequency (expressed in parts per million reads) was calculated as theproportion of sub-genome-assigned sequence reads that showed evidencefor ZFN-mediated NHEJ-directed gene editing.

From the results of three biological replicates performed for eachlinear double stranded DNA donor design, molecular evidence was obtainedfor the enrichment of sequence reads showing ZFN-mediated NHEJ-directedediting at the three homoeologous copies of the endogenous AHAS genes inwheat (Table 7 and Table 8). Strong molecular evidence was obtained forthe integration of the linear, double-stranded 41-bp donor molecule atthe position of the double strand DNA break created by cleavage of thehomoeologous copies of the AHAS gene by ZFNs 29732 and 29730 in samplesof both SEC protoplasts and scutella of immature zygotic embryos thatwere transfected with pDAB109350 and pDAS000152. Similar editingefficiency was observed across the three wheat sub-genomes in thesesamples. In contrast, samples of SEC protoplasts and scutella ofimmature zygotic embryos transfected with pDAB109350 and pDAS000153showed poor evidence for ZFN-mediated NHEJ-directed gene editing,presumably due to the prerequisite requirement for in planta release ofthe 41-bp donor sequence from the plasmid backbone. Molecular evidencefor the replacement of endogenous AHAS sequence with the 41-bp donormolecule was observed in both SEC protoplasts and scutella of immaturezygotic embryos that were transfected with pDAB109350, pDAB109360 andpDAS000149. However, the frequency of editing was significantly lowerthan that observed for transfections performed using pDAB109350 andpDAS000152, presumably due to the requirement for dual ZFN cleavage ofthe endogenous AHAS sequence. Limited evidence was obtained for thereplacement of endogenous AHAS sequence with the 41-bp donor moleculethat required in planta release from plasmid backbone in samples of SECprotoplast and scutella of immature zygotic embryos that weretransfected with pDAB109350, pDAB109360 and pDAS000150.

TABLE 7 Average NHEJ editing frequency in parts per million (ppm) acrossthree biological replicates of scutella transfected with lineardouble-stranded donor DNA designs. Donor- Editing to-ZFN Frequency inEditing molar Wheat Sub- Frequency Donor ZFN ratio Genome (ppm)pDAS000152 n/a n/a A 0 29732-2A- pDAS000152 29730 5:1 A 0 29732-2A-pDAS000152 29730 10:1 A 131 pDAS000152 n/a n/a B 0 29732-2A- pDAS00015229730 5:1 B 0 29732-2A- pDAS000152 29730 10:1 B 47 pDAS000152 n/a n/a D0 29732-2A- pDAS000152 29730 5:1 D 0 29732-2A- pDAS000152 29730 10:1 D75 pDAS000153 n/a n/a A 0 29732-2A- pDAS000153 29730 5:1 A 4 29732-2A-pDAS000153 29730 10:1 A 0 pDAS000153 n/a n/a B 0 29732-2A- pDAS00015329730 5:1 B 0 29732-2A- pDAS000153 29730 10:1 B 0 pDAS000153 n/a n/a D 029732-2A- pDAS000153 29730 5:1 D 0 29732-2A- pDAS000153 29730 10:1 D 0pDAS000149 n/a n/a A 0 29732-2A- pDAS000149 29730 5:1 A 23 29732-2A-pDAS000149 29730 10:1 A 9 pDAS000149 n/a n/a B 0 29732-2A- pDAS00014929730 5:1 B 7 29732-2A- pDAS000149 29730 10:1 B 3 pDAS000149 n/a n/a D 029732-2A- pDAS000149 29730 5:1 D 7 29732-2A- pDAS000149 29730 10:1 D 0pDAS000150 n/a n/a A 0 29732-2A- pDAS000150 29730 5:1 A 1 29732-2A-pDAS000150 29730 10:1 A 0 pDAS000150 n/a n/a B 0 29732-2A- pDAS00015029730 5:1 B 0 29732-2A- pDAS000150 29730 10:1 B 0 pDAS000150 n/a n/a D 029732-2A- pDAS000150 29730 5:1 D 4 29732-2A- pDAS000150 29730 10:1 D 0pDAS000150 n/a n/a A 0 “na” indicates “not applicable.”

TABLE 8 Average NHEJ editing frequency in parts per million (ppm) acrossthree biological replicates of SEC protoplast transfected with lineardouble-stranded donor DNA designs. Donor- Editing to-ZFN Frequency inEditing molar Wheat Sub- Frequency Donor ZFN ratio Genome (ppm)pDAS000152 n/a n/a A 0 29732-2A- pDAS000152 29730 5:1 A 0 29732-2A-pDAS000152 29730 10:1 A 6717 29732-2A- pDAS000152 29730 20:1 A 5404pDAS000152 n/a n/a B 0 29732-2A- pDAS000152 29730 5:1 B 0 29732-2A-pDAS000152 29730 10:1 B 6306 29732-2A- pDAS000152 29730 20:1 B 4106pDAS000152 n/a n/a D 0 29732-2A- pDAS000152 29730 5:1 D 0 29732-2A-pDAS000152 29730 10:1 D 7911 29732-2A- pDAS000152 29730 20:1 D 4059pDAS000153 n/a n/a A 0 29732-2A- pDAS000153 29730 5:1 A 0 29732-2A-pDAS000153 29730 10:1 A 0 29732-2A- pDAS000153 29730 20:1 A 0 pDAS000153n/a n/a B 0 29732-2A- pDAS000153 29730 5:1 B 0 29732-2A- pDAS00015329730 10:1 B 0 29732-2A- pDAS000153 29730 20:1 B 0 pDAS000153 n/a n/a D0 29732-2A- pDAS000153 29730 5:1 D 0 29732-2A- pDAS000153 29730 10:1 D 029732-2A- pDAS000153 29730 20:1 D 0 pDAS000153 n/a n/a A 0 29732-2A-pDAS000153 29730 5:1 A 0 pDAS000149 n/a n/a A 0 29732-2A- pDAS00014929730 5:1 A 0 29732-2A- pDAS000149 29730 10:1 A 0 29732-2A- pDAS00014929730 20:1 A 344 pDAS000149 n/a n/a B 0 29732-2A- pDAS000149 29730 5:1 B0 pDAS000149 29732-2A- 10:1 B 0 29730 29732-2A- pDAS000149 29730 20:1 B210 pDAS000149 n/a n/a D 0 29732-2A- pDAS000149 29730 5:1 D 4 29732-2A-pDAS000149 29730 10:1 D 0 29732-2A- pDAS000149 29730 20:1 D 24pDAS000150 n/a n/a A 0 29732-2A- pDAS000150 29730 5:1 A 0 29732-2A-pDAS000150 29730 10:1 A 0 29732-2A- pDAS000150 29730 20:1 A 0 pDAS000150n/a n/a B 0 29732-2A- pDAS000150 29730 5:1 B 0 29732-2A- pDAS00015029730 10:1 B 0 29732-2A- pDAS000150 29730 20:1 B 0 pDAS000150 n/a n/a D0 29732-2A- pDAS000150 29730 5:1 D 0 29732-2A- pDAS000150 29730 10:1 D 029732-2A- pDAS000150 29730 20:1 D 0 “na” indicates “not applicable.”

Collectively, the results provide strong molecular evidence for preciseZFN-mediated NHEJ-directed editing at the endogenous AHAS gene locus inwheat. These results show that all three sub-genomes can be targetedwith a single ZFN and donor. The results clearly demonstrate a higherfrequency of editing for linear donor DNA designs as compared to plasmiddonor DNA designs. Presumably, these results are due to the prerequisiterequirement for in planta linearization of the plasmid donor moleculesbefore they can participate in NHEJ-directed DNA repair. The resultsalso indicate that sub-genome-specific mediated NHEJ-directed geneediting is facilitated by a double strand break. The ZFNs that weredesigned to induce the double strand DNA breaks resulted in asub-genome-specific mediated NHEJ-directed gene editing when deliveredwith the donor DNA to the Triticum aestivum plant cells.

Example 5 Development of a Transformation System for Producing AHASEdited Plants

The endogenous AHAS gene locus in wheat was selected as a model locus todevelop a transformation system for generating plants with precisegenome modifications induced by ZFN-mediated gene editing. Theendogenous AHAS gene was selected as a model locus due to its ability toproduce a selectable phenotype (i.e., tolerance to group B herbicides,or ALS inhibitor herbicides such as imidazolinone or sulfonylurea),knowledge of prerequisite information of sub-genome-specific gene codingsequence, and knowledge of specific mutations conferring tolerance togroup B herbicides, or ALS inhibitor herbicides from thecharacterization of wheat with chemically induced mutations in the AHASgenes. The S653N mutation conferring tolerance to imidazolinone classherbicide was chosen as a target for ZFN-mediated gene editing due tothe availability of commercially released wheat varieties carrying theS653N mutation that could be used as positive controls to develop achemical selection system to enrich for precisely edited events.

Molecular Characterization of Triticum aestivum Cv. Clearfield Janz

Triticum aestivum cv. Clearfield Janz, a commercially released breadwheat variety carrying the S653N mutation in the D-genome, was selectedfor use as a positive control to develop a chemical selection strategyto enrich for AHAS edited wheat plants produced by ZFN-mediated geneediting. To generate a pure genetic seed stock, 48 seedlings werescreened with 96 microsatellite (SSR) markers using Multiplex-Ready PCRtechnology (Hayden et al., (2008) BMC Genomics 9; 80). Seedlings withidentical SSR haplotypes were used to produce seed that was used insubsequent experiments.

To ensure that the wheat plants used to produce seed carried the S653Nmutation, a PCR assay was developed to amplify the region of the AHASgene carrying the mutation from the D-genome of wheat.Sub-genome-specific amplification was achieved using on-off PCR (Yang etal., (2005) Biochemical and Biophysical Research Communications328:265-72) with primers AHAS-PS-6DF2 and AHAS-PS-6DR2 (SEQ ID NO: 82and SEQ ID NO: 83) designed to position the penultimate base (whichcontained a phosphorothioate linkage) over nucleotide sequence variationthat distinguished between the homoeologous copies of the AHAS genes.The PCR primers were designed to be between 18 and 27 nucleotides inlength and to have a melting temperature of 60 to 65° C., optimal 63° C.The amplified PCR products were purified using a QIAQUICK MINIELUTE PCRPURIFICATION KIT™ (Qiagen) and sequenced using a direct Sangersequencing method. The sequencing products were purified with ethanol,sodium acetate and EDTA following the BIGDYE® v3.1 protocol (AppliedBiosystems) and electrophoresis was performed on an ABI3730XL® automatedcapillary electrophoresis platform.

Analysis of the amplified AHAS gene sequences using SEQUENCHER v3.7™(GeneCodes, Ann Arbor, Mich.) revealed segregation for the S653Nmutation and enabled the identification of plants that were homozygous(N653/N653) and heterozygous (N653/S653) for the S653N mutation orhomozygous (S653/S653) for the herbicide-susceptible allele. The harvestof seed from individual plants provided a seed source having differentlevels of zygosity for the S653N mutation in the cv. Clearfield Janzgenetic background.

Optimization of Chemical Selection Conditions Based on IMAZAMOX™

A series of experiments were performed to determine optimal selectionconditions for regenerating AHAS edited wheat plants. These experimentswere based on testing the basal tolerance to IMAZAMOX™ of the donorwheat line cv. Bobwhite MPB26RH (S653/S653 genotype) at the callusinduction, plant regeneration and rooting stages of an established wheattransformation system. Similar experiments were performed to determinethe basal tolerance and resistance of cv. Clearfield Janz genotypescarrying the different doses of the S653N mutation; i.e., plants withN653/N653 and S653/S653 genotypes.

The basal tolerance of the donor wheat line cv. Bobwhite MPB26RH andbasal resistance of cv. Clearfield Janz (N653/N653) genotype toIMAZAMOX® at the callus induction stage was determined as follows:Scutella of immature zygotic embryos from each wheat line were isolatedas described previously and placed in 10 cm PETRI™ dishes containing CIMmedium supplemented with 0, 50, 100, 200, 300, 400 and 500 nM IMAZAMOX®respectively. Twenty scutella were placed in each PETRI™ dish. A totalof 60 scutella from each of the donor wheat line cv. Bobwhite MPB26RHand cv. Clearfield Janz genotype were tested for basal tolerance andbasal resistance response, respectively, at each IMAZAMOX®concentration. After incubation at 24° C. in the dark for 4 weeks, theamount of somatic embryogenic callus formation (SEC) at each IMAZAMOX®concentration was recorded. The results showed that SEC formation forcv. Bobwhite MPB26RH was reduced by about 70% at 100 nM IMAZAMOX®,compared to untreated samples. Callus formation for the cv. ClearfieldJanz genotype was unaffected, relative to the untreated control, at anyIMAZAMOX® concentrations tested.

The basal tolerance of the donor wheat line cv. Bobwhite MPB26RH toIMAZAMOX® at the plant regeneration stage was determined as follows:Scutella of immature zygotic embryos from the donor wheat line wereisolated as described previously and placed in 10 cm PETRI™ dishescontaining CIM medium. Somatic embryogenic callus was allowed to form byincubating at 24° C. in the dark for 4 weeks. The SEC was transferred to10 cm PETRI™ dishes containing DRM medium supplemented with 0, 100, 200,300, 400, 500 and 1000 nM IMAZAMOX® respectively. Twenty CIM were placedin each PETRI™ dish. A total of 60 CIM were tested for basal toleranceresponse at each IMAZAMOX® concentration. After incubation for 2 weeksat 24° C. under a 16/8 (light/dark) hour photoperiod in a growth room,the regeneration response was recorded. The results showed that plantregeneration was reduced by about 80% at 200 nM IMAZAMOX®, compared tountreated samples.

The basal tolerance of the cv. Clearfield Janz (S653/S653) genotype andbasal resistance of the cv. Clearfield Janz (N653/N653) genotype toIMAZAMOX® at the plant regeneration stage was determined using amodified approach, as cv. Clearfield Janz was observed to have poorplant regeneration response (i.e., poor embryogenesis) in tissueculture. Seed for each cv. Clearfield Janz genotype was germinated usingthe aseptic approach described above for producing wheat mesophyllprotoplasts. The germinated seedlings were multiplied in vitro bysub-culturing on multiplication medium. Following multiplication, plantsfor each genotype were transferred to 10 cm PETRI™ dishes containingplant growth medium (MS+10 μM BA+0.8% agar) supplemented with 0, 100,300, 600, 900, 1200, 1500 and 3000 nM IMAZAMOX®, respectively. Tenplants were placed in each PETRI™ dish. A total of 30 plants pergenotype were tested for basal response at each IMAZAMOX® concentration.After incubation for 3 weeks at 24° C. under a 16/8 (light/dark) hourphotoperiod in a growth room, the growth response was recorded. Theresults showed that plant growth for the cv. Clearfield Janz (S653/S653)genotype was severely reduced in medium containing at least 200 nMIMAZAMOX®, compared to untreated samples. This response was similar tothat observed for the cv. Bobwhite MPB26RH (S653/S653) genotype. Incontrast, plant growth for the cv. Clearfield Janz (N653/N653) genotypewas not strongly suppressed, relative to untreated samples, until theIMAZAMOX® concentration exceeded 2,000 nM.

The basal tolerance of the donor wheat line cv. Bobwhite MPB26RH toIMAZAMOX® at the plant rooting stage was determined as follows: Scutellaof immature zygotic embryos from the donor wheat line were isolated asdescribed previously and placed in 10 cm PETRI™ dishes containing CIMmedium. Somatic embryogenic callus was allowed to form by incubating at24° C. in the dark for 4 weeks. The SEC was transferred to 10 cm PETRI™dishes containing DRM medium and incubated for 2 weeks at 24° C. under a16/8 (light/dark) hour photoperiod to allow plant regeneration to takeplace. Regenerated plants were transferred to 10 cm PETRI™ dishescontaining RM medium supplemented with 0, 100, 200, 300, 400, 500 nMIMAZAMOX®, respectively. Twenty regenerated plants were placed in eachPETRI™ dish. A total of 60 regenerated plants were tested for basaltolerance response at each IMAZAMOX® concentration. After incubation for3 weeks at 24° C. under a 16/8 (light/dark) hour photoperiod in a growthroom, the root formation response was recorded. The results showed thatroot formation was severely restricted at all concentrations ofIMAZAMOX® tested, compared to untreated samples.

The basal tolerance of the cv. Clearfield Janz (S653/S653) genotype andbasal resistance of the cv. Clearfield Janz (N653/N653) genotype toIMAZAMOX® at the plant rooting stage was determined using a modifiedapproach, as cv. Clearfield Janz was observed to have poor plantregeneration response (i.e., poor embryogenesis) in tissue culture. Seedfor each cv. Clearfield Janz genotype was germinated using the asepticapproach described above for producing wheat mesophyll protoplasts. Thegerminated seedlings were multiplied in vitro by sub-culturing onmultiplication medium. Following multiplication, plants for eachgenotype were transferred to 10 cm PETRI™ dishes containing plantrooting medium (½ MS, 0.5 mg/L NAA, 0.8% agar) supplemented with 0, 50,100, 200 and 250 nM IMAZAMOX®, respectively. Three plants were placed ineach PETRI™ dish. A total of 6 plants per genotype were tested for basalresponse at each IMAZAMOX® concentration. After incubation for 2 weeksat 24° C. under a 16/8 (light/dark) hour photoperiod in a growth room,the root formation response was recorded.

The results showed that root formation for the cv. Clearfield Janz(N653/N653) genotype was restricted, compared to untreated samples, at250 nM IMAZAMOX®. Root formation was severely restricted in the cv.Clearfield Janz (S653/S653) genotype at all concentrations of IMAZAMOX®tested, compared to untreated samples.

Design and Synthesis of Donor DNA for ZFN-Mediated NHEJ-Directed AHASGene Editing

Two types of donor DNA molecule were designed to promote preciseZFN-mediated NHEJ-directed gene editing at the endogenous AHAS genes inwheat. Both donor designs allowed for the introduction of the S653Nmutation known to confer tolerance to imidazolinone class herbicides (Liet al., (2008) Molecular Breeding 22:217-225).

The first design was based on the integration of a 95-bp double strandeddonor molecule at the position of the double strand DNA break created bycleavage of a homoeologous copy of the endogenous AHAS gene by ZFNs29732 and 29730 (encoded on plasmid pDAB109350). The donor DNA molecule,pDAS000267 (SEQ ID NO:84 and SEQ ID NO:85), comprised two portions ofthe integrating donor polynucleotide. The 5′ end contained sequence nearidentical to the endogenous AHAS gene encoded in the D-genome, startingfrom the target ZFN cleavage site and finishing at the AHAS stop codon.Six intentional mutations were introduced into this sequence: twomutations encoded the S653N mutation (AGC→AAT), and four mutations weresynonymous (in which a silent mutation was incorporated into the donorsequence). The 3′ end of the donor molecule contained a unique sequencethat could be used for diagnostic PCR to detect ZFN-mediatedNHEJ-directed gene editing events. The donor molecule was designed withprotruding 5′ and 3′ ends to provide ligation overhangs to facilitateZFN-mediated NHEJ-directed DNA repair.

The second design was based on replacement of the endogenous AHASsequence located between a pair of ZFN target sites with a 79-bp doublestranded donor molecule. Specifically, the donor was designed to replacethe endogenous AHAS sequence released from chromatin upon dual cleavageof a homoeologous copy of the AHAS gene by ZFNs 29732 and 29730 (encodedon plasmid pDAB109350) and ZFNs 30012 and 30018 (encoded on plasmidpDAB109360). The donor molecule, pDAS000268 (SEQ ID NO:86 and SEQ IDNO:87), comprised sequence near identical to the endogenous AHAS geneencoded in the D-genome, starting from the cleavage site for ZFNs 29732and 29730, and finishing at the cleavage site for ZFNs 30012 and 30018.Ten deliberate mutations were introduced into this sequence. Sixmutations were located at the 5′ end of the donor: two mutations encodedthe S653N mutation (AGC→AAT) and four mutations were synonymous. Fourmutations were located at the 3′ end of the donor and were located innon-coding sequence. The donor molecule was designed with protruding 5′and 3′ ends to provide ligation overhangs to facilitate ZFN-mediatedNHEJ-directed DNA repair.

Standard phosphoramidite chemistry was used to synthetically synthesizethe double stranded DNA donor molecules (Integrated DNA Technologies).For each donor molecule, a pair of complementary single stranded DNAoligomers was synthesized, each with two phosphorothioate linkages attheir 5′ ends to provide protection against in planta endonucleasedegradation. The single stranded DNA oligomers were purified by highperformance liquid chromatography to enrich for full-length moleculesand purified of chemical carryover from the synthesis steps using Na⁺exchange. The double stranded donor molecule was formed by annealingequimolar amounts of the two complementary single-stranded DNA oligomersusing standard methods commonly known by one skilled in the art. Beforedelivery to Triticum aestivum, the double stranded DNA molecules werediluted to the required concentration in sterile water.

Design and Production of Binary Vector Encoding AHAS (S653N)

Standard cloning methods were used in the construction of binary vectorpDAS000143 (SEQ ID: 88) (FIG. 10). The AHAS (S653N) gene expressioncassette consists of the promoter, 5′ untranslated region and intronfrom the Ubiquitin (Ubi) gene from Zea mays (Toki et al., (1992) PlantPhysiology 100; 1503-07) followed by the coding sequence (1935 bp) ofthe AHAS gene from T. aestivum with base-pairs 1880 and 1181 mutatedfrom CG to AT in order to induce an amino acid change from serine (S) toaspargine (N) at amino acid residue 653. The AHAS expression cassetteincluded the 3′ untranslated region (UTR) of the nopaline synthase gene(nos) from A. tumefaciens pTi15955 (Fraley et al., (1983) Proceedings ofthe National Academy of Sciences U.S.A. 80(15); 4803-4807). Theselection cassette was comprised of the promoter, 5′ untranslated regionand intron from the actin 1 (Act1) gene from Oryza sativa (McElroy etal., (1990) The Plant Cell 2(2); 163-171) followed by a synthetic,plant-optimized version of phosphinothricin acetyl transferase (PAT)gene, isolated from Streptomyces viridochromogenes, which encodes aprotein that confers resistance to inhibitors of glutamine synthetasecomprising phosphinothricin, glufosinate, and bialaphos (Wohlleben etal., (1988) Gene 70(1); 25-37). This cassette was terminated with the 3′UTR from the 35S gene of cauliflower mosaic virus (CaMV) (Chenault etal., (1993) Plant Physiology 101 (4); 1395-1396).

The selection cassette was synthesized by a commercial gene synthesisvendor (GeneArt, Life Technologies) and cloned into a Gateway-enabledbinary vector with the RfA Gateway cassette located between theUbiquitin (Ubi) gene from Zea mays and the 3′ untranslated region (UTR)comprising the transcriptional terminator and polyadenylation site ofthe nopaline synthase gene (nos) from A. tumefaciens pTi15955. The AHAS(S653N) coding sequence was amplified with flanking attB sites andsub-cloned into pDONR221. The resulting ENTRY clone was used in a LRCLONASE II™ (Invitrogen, Life Technologies) reaction with theGateway-enabled binary vector encoding the phosphinothricin acetyltransferase (PAT) expression cassette. Colonies of E. coli cellstransformed with all ligation reactions were initially screened byrestriction digestion of miniprep DNA. Restriction endonucleases wereobtained from New England BioLabs and Promega. Plasmid preparations wereperformed using the QIAPREP SPIN MINIPREP KIT™ or the PURE YIELD PLASMIDMAXIPREP SYSTEM™ (Promega Corporation, WI) following the manufacturer'sinstructions. Plasmid DNA of selected clones was sequenced using ABISanger Sequencing AND BIG DYE TERMINATOR v3.1™ cycle sequencing protocol(Applied Biosystems, Life Technologies). Sequence data were assembledand analyzed using the SEQUENCHER™ software (Gene Codes Corporation, AnnArbor, Mich.).

Biolistic-Mediated Transformation System for Generating AHAS EditedWheat Plants

About 23,000 scutella of immature zygotic embryos from the donor wheatline cv. Bobwhite MPB26RH were prepared for biolistics-mediated DNAdelivery, as described previously. DNA-coated gold particles wereprepared as described above with the following formulations. Fortransfections performed using pDAS000267, the donor DNA was mixed at a5:1 molar ratio with plasmid DNA for pDAB109350 (encoding ZFNs 29732 and29730). For transfections performed using pDAS000268, the donor DNA wasmixed at a 10:1:1 molar ratio with plasmid DNA for pDAB109350 (encodingZFNs 29732 and 29730) and pDAB109360 (encoding ZFNs 30012 and 30018).Transfections performed using pDAS000143 were performed using goldparticles that were coated only with plasmid DNA for pDAS000143.

Biolistic-mediated transfections were performed as described previously.A total of 15,620 scutella were bombarded with gold particles coatedwith DNA containing pDAS000267, a total of 7,310 scutella were bombardedwith gold particles coated with DNA containing pDAS000268, and a totalof 2,120 scutella were bombarded with gold particles coated withpDAS000143. Following bombardment, the transfected scutella wereincubated at 26° C. in the dark for 16 h before being transferred ontomedium for callus induction.

Four different chemical selection strategies based on IMAZAMOX® wereused to enrich for regenerated wheat plants that had the S653N mutationprecisely integrated into one or more homoeologous copies of theendogenous AHAS gene by ZFN-mediated NHEJ-directed gene editing. Thefour chemical selection strategies are described in Table 9. For eachstrategy, scutella were cultured in the dark on callus induction mediumat 24° C. for 2 weeks. The resultant calli were sub-cultured once ontofresh callus induction medium and kept in the same conditions for afurther two weeks. Somatic embryogenic callus (SEC) was transferred ontoplant regeneration medium and cultured for 2 weeks at 24° C. under a16/8 (light/dark) hour photoperiod in a growth room. Regeneratedplantlets were transferred onto rooting medium and cultured under thesame conditions for 2-3 weeks. To increase stringency for the selectionof regenerated plants having the S653N mutation, the roots ofregenerated plants were removed and the plants were again sub-culturedon rooting media under the same conditions. Plantlets rooting a secondtime were transferred to soil and grown under glasshouse containmentconditions. T₁ seed was harvested from individual plants, followingbagging of individual spikes to prevent out-crossing.

The scutella explants bombarded with gold particles coated withpDAS000143 were used to monitor the selection stringency across the fourchemical selection strategies for regenerating wheat plants carrying theAHAS S653N mutation. Plants transformed with pDAS000143 were regeneratedusing process described above.

TABLE 9 Chemical selection strategies used to regenerate wheat plantsthat had the S653N mutation precisely integrated into one or morehomoeologous copies of the endogenous AHAS gene by ZFN-mediatedNHEJ-directed gene editing. Plant Regeneration Stage Strategy 1 Strategy2 Strategy 3 Strategy 4 Callus induction 150 nM IMI 250 nM IMI 150 nMIMI 250 nM IMI (CIM) Plant Regeneration 150 nM IMI  0 nM IMI 250 nM IMI250 nM IMI (DRM) Rooting (RM) 200 nM IMI 200 nM IMI 200 nM IMI 200 nMIMI (IMI = IMAZAMOX ™)

Overall, 14 putatively ZFN-mediated NHEJ-directed AHAS edited wheatplants were recovered from the transfection of 22,930 scutella ofimmature zygotic embryos from the donor wheat line cv. Bobwhite MPB26RH.Putatively edited plants were obtained from all four selectionstrategies for scutella bombarded with gold particles coated with DNAcontaining pDAS000267. Two putatively edited plants were obtained fromthe second selection strategy for scutella bombarded with gold particlescoated with DNA containing pDAS000268. A total of 129 putativelytransformed wheat plants carrying at least one randomly integrated copyof the AHAS (S653N) donor polynucleotide were recovered across the fourchemical selection strategies.

Example 6 Molecular Characterization of Edited Wheat Plants

The wheat plants resulting from bombardments with a donor polynucleotideencoding the S653N mutation were obtained and molecularly characterizedto identify the wheat sub-genomes that comprised an integration of theS653N mutation that occurred as a result of the donor integration at agenomic double strand cleavage site. Two series of bombardments werecompleted. The first set of experiments was completed with pDAS000143,and the second set of experiments was completed with pDAS000267 andpDAS000268. Individual wheat plants were obtained from both sets ofexperiments and assayed via a molecular method to identify plants whichcontained an integrated copy of the AHAS donor polynucleotide encodingthe S653N mutation.

A hydrolysis probe assay (analogous to the TAQMAN® based assay) forquantitative PCR analysis was used to confirm that recovered wheatplants that had been bombarded with pDAS000143 carried at least onerandomly integrated copy of the AHAS donor polynucleotide encoding theS653N mutation. Confirmation via Sanger sequence analysis indicated thatwheat plants recovered from bombardments performed with pDAS000267 andpDAS000268 comprised the S653N donor polynucleotide in at least one ofthe homoeologous copies of the AHAS gene at the position expected forZFN-mediated NHEJ-directed gene editing.

Genomic DNA Isolation from Regenerated Wheat Plants

Genomic DNA was extracted from freeze-dried leaf tissue harvested fromeach regenerated wheat plant. Freshly harvested leaf tissue was snapfrozen in liquid nitrogen and freeze-dried for 24 h in a LABCONCOFREEZONE 4.5® (Labconco, Kansas City, Mo.) at −40° C. and 133×10⁻³ mBarpressure. The lyophilized material was subjected to DNA extraction usingthe DNEASY® PLANT DNA EXTRACTION MINI KIT™ (Qiagen) following themanufacturer's instructions.

PCR Assay to Confirm Random Integration of AHAS Donor PolynucleotideEncoding S653N Mutation

To confirm that the regenerated wheat plants from bombardments performedwith pDAS000143 carried at least one randomly integrated copy of theAHAS donor polynucleotide encoding the S653N mutation, a duplexhydrolysis probe qPCR assay (analogous to TAQMAN®) was used to amplifythe endogenous single copy gene, puroindoline-b (Pinb), from the Dgenome of hexaploid wheat (Gautier et al., (2000) Plant Science 153,81-91; SEQ ID NO: 89, SEQ ID NO: 90 and SEQ ID NO: 91 for forward andreverse primers and probe sequence, respectively) and a region of theActin (Act1) promoter present on pDAS000143 (SEQ ID NO: 92, SEQ ID NO:93 and SEQ ID NO: 94 for forward and reverse primers and probe sequence,respectively). Hydrolysis probe qPCR assays were performed on 24randomly chosen wheat plants that were recovered from each of the fourchemical selection strategies. Assessment for the presence, andestimated copy number of pDAS00143 was performed according to the methoddescribed in Livak and Schmittgen (2001) Methods 25(4):402-8.

From the results, conclusive evidence was obtained for the integrationof at least one copy of the AHAS donor polynucleotide encoding the S653Nmutation into the genome of each of the wheat plants tested. Theseresults indicate that the four chemical selection strategies providedstringent selection for the recovery of plants expressing the S653Nmutation.

PCR Assay of Genomic DNA for ZEN-Mediated AHAS Editing

To characterize the sub-genomic location and outcome of ZFN-mediatedNHEJ-directed gene editing in the recovered wheat plants, PCR withprimers AHAS_(—)3F1 and AHAS_(—)3R1 (SEQ ID NO:95 and SEQ ID NO:96) wasused to amplify the target region from the homoeologous copies of theAHAS genes. The resulting PCR products were cloned into plasmid vectorand Sanger sequenced using BIGDYE® v3.1 chemistry (Applied Biosystems)on an ABI3730XL® automated capillary electrophoresis platform. Sangersequencing of up to 120 independent plasmid clones was performed toensure that each allele at the endogenous AHAS homoeologs was sequenced.Sequence analysis performed using SEQUENCHER SOFTWARE™ was used togenerate a consensus sequence for each allele of the three homoeologouscopies of the AHAS gene in each of the recovered wheat plants, and todetermine the sub-genomic origin and sequence for each edited allele.

From the results, conclusive evidence for precise ZFN-mediatedNHEJ-directed gene editing at the endogenous AHAS loci was demonstratedfor 11 of the 12 recovered wheat plants that were transformed usingpDAB109350 and pDAS000267 (Table 10), and both of the recovered wheatplants that were transformed using pDAB109350, pDAB109360 and pDAS000268(Table 11). Plants with a range of editing outcomes were observedincluding: (1) independent events with perfect sub-genome-specificallele edits; (2) events with single perfect edits in the A-genome,B-genome and D-genomes; (3) events with simultaneous editing in multiplesub-genomes; and, (4) events demonstrating hemizygous and homozygoussub-genome-specific allele editing. Disclosed for the first time is amethod which can be utilized to mutate a gene locus within all threegenomes of a wheat plant. Wheat plants comprising an integrated AHASdonor polynucleotide encoding a S653N mutation are exemplified;integration of the polynucleotide sequence provides tolerance toimidazolinone class herbicides. The utilization of ZFN-mediated genomicediting at an endogenous gene locus in wheat allows for the introductionof agronomic traits (via mutation) without time consuming wheat breedingtechniques which require backcrossing and introgression steps that canincrease the amount of time required for introgressing the trait intoall three sub-genomes. Consensus Sanger sequences for the allelespresent in each sub-genome for the edited wheat plants are provided asSEQ ID NO:97-180 in Tables 10 and 11.

TABLE 10 ZFN-mediated NHEJ-directed AHAS editing outcomes for wheatplants transformed using pDAB109350 and pDAS000267 A-genome B-genomeD-genome Allele 1 Allele 2 Allele 1 Allele 2 Allele 1 Allele 2 SEQ IDNO: Plant Status PE NHEJ IE UE IE UE  97-102 No. 1 No. 13 20 12 19 14 22clones¹ Plant Status NHEJ UE UE nd IE UE 103-108 No. 2 No.  9  3 16  075 17 clones¹ Plant Status PE UE UE nd UE nd 109-114 No. 3 No.  7 11 29 0 35  0 clones¹ Plant Status PE UE IE UE PE IE 115-120 No. 4 No.  6 1144 30  6 11 clones¹ Plant Status PE UE NHEJ UE UE nd 121-126 No. 5 No.10  9 15 26 21  0 clones¹ Plant Status UE nd PE UE UE nd 127-132 No. 6No. 22  0 11 18 43  0 clones¹ Plant Status PE UE UE nd UE nd 133-138 No.7 No.  5 12 26  0 22  0 clones¹ Plant Status UE nd UE nd UE nd 139-144No. 8 No. 32  0 40  0 26  0 clones¹ Plant Status PE nd IE UE UE nd145-150 No. 9 No. 24  0 13 21 33  0 clones¹ Plant Status PE UE UE nd UEnd 151-156 No. 10 No. 10 19 37  0 29  0 clones¹ Plant Status UE nd UE ndPE UE 157-162 No. 11 No. 35  0 37  0 15 11 clones¹ Plant Status UE nd UEnd IE NHEJ 163-168 No. 12 No. 34  0 40  0 14  8 clones¹ ¹Number ofindependent plasmid clones sequenced. PE = perfect edit; i.e.,ZFN-mediated NHEJ-directed genome editing produced a predicted outcome.IE = imperfect edit; i.e., ZFN-mediated NHEJ-directed genome editingproduced an unpredicted outcome. UE = unedited allele; i.e., allele hadwild-type sequence. nd = not detected; i.e., sufficient independentplasmid clones were sequenced to conclude that an alternate allele wasnot present and that the locus was homozygous for a single allele. NHEJ= Non Homologous End Joining; i.e., evidence for a non-homologous endjoining DNA repair outcome that did not result in the integration of adonor molecule at the ZFN cleavage site.

TABLE 11 ZFN-mediated NHEJ-directed AHAS editing outcomes for wheatplants transformed using pDAB109350, pDAB109360 and pDAS000268. A-genomeB-genome D-genome Allele 1 Allele 2 Allele 1 Allele 2 Allele 1 Allele 2SEQ ID NO: Plant Status IE UE UE nd IE nd 169-174 No. 12a No.  5 14 53 0 1 24 clones¹ Plant Status IE UE UE nd UE nd 175-180 No. 13a No. 10 1249 0 18  0 clones¹ ¹Number of independent plasmid clones sequenced. IE =imperfect edit; i.e., ZFN-mediated NHEJ-directed genome editing producedunexpected outcome. UE = unedited allele; i.e., allele had wild-typesequence. nd = not detected; i.e., sufficient independent plasmid cloneswere sequenced to conclude that an alternate allele was not present andthat the locus was homozygous for a single allele.

Example 7 Design of Zinc Finger Binding Domains Specific to Region inAHAS Genes Encoding the P197 Amino Acid Residue

Zinc finger proteins directed against DNA sequence of the homoeologouscopies of the AHAS genes were designed as previously described (see alsoExample 2). Exemplary target sequence and recognition helices are shownin Table 12 (recognition helix regions designs) and Table 13 (targetsites). In Table 13, nucleotides in the target site that are contactedby the ZFP recognition helices are indicated in uppercase letters;non-contacted nucleotides are indicated in lowercase. Zinc FingerNuclease (ZFN) target sites were upstream (from 2 to 510 nucleotidesupstream) of the region in the AHAS gene encoding the proline 197 (P197)amino acid residue.

TABLE 12  AHAS zinc finger designs (N/A indicates “Not Applicable”) ZFP#F1 F2 F3 F4 F5 F6 34456 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ IDNO: 227 NO: 182 NO: 182 NO: 236 NO: 237 NO: 182 RSADLTR RSDDLTR RSDDLTRRSDALTQ ERGTLAR RSDDLTR 34457 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/ANO: 184 NO: 238 NO: 182 NO: 239 NO: 240 QSGDLTR DTGARLK RSDDLTR HRRSRDQDRSYRNT 34470 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 241 NO: 242NO: 243 NO: 233 NO: 244 RSADLSR RSDHLSA QSSDLRR DRSNLSR RSDDRKT 34471SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 184 NO: 245 NO: 182NO: 246 NO: 227 NO: 247 QSGDLTR RRADRAK RSDDLTR TSSDRKK RSADLTR RNDDRKK34472 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 227 NO: 198 NO: 237NO: 182 NO: 218 NO: 248 RSADLTR DRSNLTR ERGTLAR RSDDLTR DRSDLSR DSSTRRR34473 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 219 NO: 249 NO: 210  NO: 250 NO: 237  NO: 224 RSDHLSE HSRTRTK RSDTLSE NNRDRTKERGTLAR DRSALAR 34474 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 237NO: 182 NO: 218 NO: 248 NO: 198 ERGTLAR RSDDLTR DRSDLSR DSSTRRR DRSNLTR34475 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 249 NO: 73 NO: 201NO: 216 NO: 233 NO: 251 RSDHLSR QQWDRKQ DRSHLTR DSSDRKK DRSNLSR VSSNLTS34476 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 218 NO: 248  NO: 233 NO: 184 NO: 198 DRSDLSR DSSTRRR DRSNLSR QSGDLTR DRSNLTR 34477 SEQ IDSEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 237 NO: 249 NO: 252 NO: 253 NO: 216ERGTLAR RSDHLSR RSDALSV DSSHRTR DSSDRKK 34478 SEQ ID SEQ ID SEQ IDSEQ ID SEQ ID N/A NO: 254 NO: 255 NO: 224 NO: 256 NO: 205 RSDNLTRRSDNLAR DRSALAR DRSHLSR TSGNLTR 34479 SEQ ID SEQ ID SEQ ID SEQ ID SEQ IDSEQ ID NO: 252 NO: 253 NO: 203 NO: 254 NO: 237 NO: 224 RSDALSV DSSHRTRRSDNLSE ARTGLRQ ERGTLAR DRSALAR 34480 SEQ ID SEQ ID SEQ ID SEQ ID SEQ IDSEQ ID NO: 255 NO: 224 NO: 256 NO: 205 NO: 249 NO: 257 RSDNLAR DRSALARDRSHLSR TSGNLTR RSDHLSR TSSNRKT 34481 SEQ ID SEQ ID SEQ ID SEQ ID SEQ IDN/A NO: 224 NO: 252 NO: 253 NO: 203 NO: 254 DRSALAR RSDALSV DSSHRTRRSDNLSE ARTGLRQ 34482 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID NO: 258NO: 254 NO: 221 NO: 259 NO: 260 NO: 261 RSDDLSK RSDNLTR RSDSLSV RSAHLSRRSDALST DRSTRTK 34483 SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID N/A NO: 216NO: 259 NO: 218 NO: 219 NO: 262 DSSDRKK RSAHLSR DRSDLSR RSDHLSE TSSDRTK

TABLE 13  Target site of AHAS zinc fingers Approximate CleavageSite Relative SEQ to AHAS ZFP # and Binding ID pDAB# Pro-197Site (5′→3′) NO: pDAB111850 499-bp 34456:  263 (34456-2A- upstreamcnGCGGCCATGGCGGCG 34457) GCGagggtttg 34457:  264 acCTCcCCCGCCGTCGCAttctcnggcg pDAB111855 109-bp 34470:  265 (34470-2A- upstreamggCCGGACGCGCGGGCG 34471) tanccggacgc 34471:  266 cgTCGGCGTCTGCGTCGCCAcctccggc pDAB111856 99-bp 34472:  267 (34472-2A- upstreamacGCCGACGCGGCCgGA 34473) CGCGcgggcgt 34473:  268 gcGTCGCCaCCTCCGGCCCGGgggccac pDAB111857 96-bp 34474:  269 (34474-2A- upstreamcaGACGCCGACGCGGCC 34475) ggacgcgcggg 34475:  270 gtCGCCACcTCCGGCCCGGGGgccacca pDAB111858 90-bp 34476:  271 (34476-2A- upstreamgcGACGCAGACGCCGAC 34477) gcggccggacg 34477:  272 ccTCCGGCCCGGGGGCCaccaacctcgt pDAB111859 24-bp 34478:  273 (34478-2A- upstreamggGATGGAGTCGAGGAG 34479) ngcgtcngcga 34479:  274 tgGTCGCCATCACGGGCCAGgtcccccg pDAB111860 18-bp 34480:  275 (34480-2A- upstreamacCATGGGGATGGAGTC 34481) GAGgagngcgt 34481:  276 ccATCACGGGCCAGGTCccccgccgcat pDAB111861 16-bp 34482: 277 (34482-2A- upstreamcgACCATGGGGATGGAG 34483) TCGaggagngc 34483:  278 caTCACGGGCCAGGTCCcccgccgcatg

The AHAS zinc finger designs were incorporated into zinc fingerexpression vectors and verified for cleavage activity using a buddingyeast system, as described in Example 2. Of the numerous ZFNs that weredesigned, produced and tested to bind to the putative AHAS genomicpolynucleotide target sites, 14 ZFNs were identified as having in vivoactivity at high levels, and selected for further experimentation. All14 ZFNs were designed to bind to the three homoeologous AHAS and werecharacterized as being capable of efficiently binding and cleaving theunique AHAS genomic polynucleotide target sites in planta.

Example 8 Evaluation of Zinc Finger Nuclease Cleavage of AHAS GenesUsing Transient Assays ZFN Construct Assembly

Plasmid vectors containing ZFN expression constructs verified forcleavage activity using the yeast system (as described in Example 7)were designed and completed as previously described in Example 3. Theresulting 14 plasmid constructs: pDAB111850 (ZFNs 34456-2A-34457),pDAB111851 (ZFNs 34458-2A-34459), pDAB111852 (ZFNs 34460-2A-34461),pDAB111853 (ZFNs 34462-2A-34463), pDAB111854 (ZFNs 34464-2A-34465),pDAB111855 (ZFNs 34470-2A-34471), pDAB111856 (ZFNs 34472-2A-34473),pDAB111857 (ZFNs 34474-2A-34475), pDAB111858 (ZFNs 34476-2A-34477),pDAB111859 (ZFNs 34478-2A-34479), pDAB111860 (ZFNs 34480-2A-34481),pDAB111861 (ZFNs 34482-2A-34483), pDAB111862 (ZFNs 34484-2A-34485) andpDAB111863 (ZFNs 34486-2A-34487) were confirmed via restriction enzymedigestion and via DNA sequencing.

Preparation of DNA from ZFN Constructs for Transfection

Before delivery to Triticum aestivum protoplasts, plasmid DNA for eachZFN construct was prepared from cultures of E. coli using the PURE YIELDPLASMID MAXIPREP SYSTEM® (Promega Corporation, Madison, Wis.) or PLASMIDMAXI KIT® (Qiagen, Valencia, Calif.) following the instructions of thesuppliers.

Isolation and Transfection of Wheat Mesophyll Protoplasts

Mesophyll protoplasts from the donor wheat line cv. Bobwhite MPB26RHwere prepared and transfected using polyethylene glycol (PEG)-mediatedDNA delivery as previously described in Example 3.

PCR Assay of Protoplast Genomic DNA for ZFN Sequence Cleavage

Genomic DNA was isolated from transfected protoplasts and used for PCRassays to assess the cleavage efficiency and target site specificity ofZFNs designed to the region of the AHAS gene encoding P197, aspreviously described in Example 3. Five sets of PCR primers whichcontained a phosphorothioate linkage as indicated by the asterisk [*]were used to amplify the ZFN target site loci (Table 14). Each primerset was designed according to criteria previously described in Example3.

TABLE 14  Primer sequences used to assess AHAS ZFN cleavage efficacy andtarget site specificity. Primer SEQ ID Primer Name SetPrimer Sequence (5′→3′) NO: AHAS- Set 1a*cactctttccctacacgacgctcttccgatctTCC 279 P197ZFN.F2 CCAATTCCAACCCTCT*CAHAS- Set 1 g*tgactggagttcagacgtgtgctcttccgatctC 280 P197ZFN.R1GTCAGCGCCTGGTGGATC*T AHAS- Set 2 a*cactctttccctacacgacgctcttccgatctGC281 P197ZFN.F5 CCGTCCGAGCCCCGCA*A AHAS- Set 2g*tgactggagttcagacgtgtgctcttccgatctC 282 P197ZFN.R1 GTCAGCGCCTGGTGGATC*TAHAS- Set 3 a*cactctttccctacacgacgctcttccgatctGC 283 P197ZFN.F7GCTCGCCCGTCATCA*C AHAS- Set 3 g*tgactggagttcagacgtgtgctcttccgatctA 284P197ZFN.R5 TGGGGATGGAGTCGAGGA*G AHAS- Set 4a*cactetttccctacacgacgctcttccgatctCTT 285 P197ZFN.F9 CCGCCACGAGCAGG*GAHAS- Set 4 g*tgactggagttcagacgtgtgctcttccgatctA 286 P197ZFN.R5TGGGGATGGAGTCGAGGA*G AHAS- Set 5 a*cactctttccctacacgacgctcttccgatctTC287 P197ZFN.F11 GTCTCCGCGCTCGCTG*A AHAS- Set 5g*tgactggagttcagacgtgtgctcttccgatctTC 288 P197ZFN.R6 CACTATGGGCGTCTCCT*G

Data Analysis for Detecting NHEJ at Target ZFN Sites

Following generation of Illumina short read sequence data for samplelibraries prepared for transfected mesophyll protoplasts, bioinformaticsanalysis (as previously described in Example 3) was performed toidentify deleted nucleotides at the target ZFN sites. Such deletions areknown to be indicators of in planta ZFN activity that result fromnon-homologous end joining (NHEJ) DNA repair.

Two approaches were used to assess the cleavage efficiency andspecificity of the ZFNs tested. Cleavage efficiency was expressed (inparts per million reads) as the proportion of sub-genome assignedsequences that contained a NHEJ deletion at the ZFN target site (Table15). Rank ordering of the ZFNs by their observed cleavage efficiency wasused to identify ZFNs with the best cleavage activity for the targetregion of the AHAS genes in a sub-genome-specific manner. All of theZFNs tested showed NHEJ deletion size distributions consistent with thatexpected for in planta ZFN activity. Cleavage specificity was expressedas the ratio of cleavage efficiencies observed across the threesub-genomes.

TABLE 15 ZFN cleavage efficacy (expressed as number of NHEJ events permillion reads) and target site specificity. ZFN A-genome B-genomeD-genome pDAB111850 (34456-2A- 12,567 1,716 10,399 34457) pDAB111851(34458-2A- 2,088 995 874 34459) pDAB111852 (34460-2A- 2 2 3 34461)pDAB111853 (34462-2A- 3 0 3 34463) pDAB111854 (34464-2A- 47 92 30834465) pDAB111855 (34470-2A- 177,866 156,139 134,694 34471) pDAB111856(34472-2A- 119,857 100,300 87,770 34473) pDAB111857 (34474-2A- 248,115251,142 202,711 34475) pDAB111858 (34476-2A- 48,339 56,001 44,459 34477)pDAB111859 (34478-2A- 3,069 2,731 3,069 34479) pDAB111860 (34480-2A-11,790 11,946 11,790 34481) pDAB111861 (34482-2A- 28,719 33,888 28,71934483) pDAB111862 (34484-2A- 34485) 216 111 216 pDAB111863 (34486-2A-34487) 54 28 54

From these results, the ZFNs encoded on plasmids pDAB111855(34470-2A-34471), pDAB111856 (34472-2A-34473) and pDAB111857(34474-2A-34475) were selected for in planta targeting in subsequentexperiments, given their characteristics of significant genomic DNAcleavage activity in each of the three wheat sub-genomes.

Example 9 Artificial Crossing and Molecular Analysis to Recover Plantswith Specific Combinations of Precise Genome Modifications

Wheat events that are produced via transformation with donor DNA andzinc finger nuclease constructs result in the integration of donormolecule sequence at one or more copies of the target endogenous locus.As shown previously in Example 6, ZFN-mediated genome modificationeffectuates simultaneous editing of multiple alleles across multiplesub-genomes. Artificial crossing of transformation events can besubsequently used to select for specific combinations of precise genomemodifications. For example, artificial crossing of transformation eventsproduced in Example 5 that have precisely modified AHAS genes with theS653N mutation can be used to produce wheat plants that have the S653Nmutation in either a specific sub-genome, in any combination of multiplesub-genomes, or in all three sub-genomes.

Similarly, self-pollination of transformation events having genomemodifications at multiple copies of the target endogenous locus can besubsequently used to produce wheat events that have the S653N mutationat only a specific sub-genome. Subsequent self-pollination oftransformation events is especially useful for removing undesirablegenome modifications from an event, such as imperfect editing at one ormore copies of the target endogenous locus.

Molecular and phenotypic assays, such as those previously described, canbe used to track the inheritance of specific genome modifications in theprogeny derived from artificial crossing and self-pollination oftransformed events.

Inheritance and Expression of Precision Genome Modifications in Wheat

To verify stable expression and inheritance of the AHAS herbicidetolerance phenotype conferred by the S653N mutation carried by the wheattransformation events generated in Example 5, T1 seed from three wheatevents were subjected to molecular and phenotypic analysis. The threeindependent wheat events each carried the integrated S653N mutation inthe AHAS gene located within the A-genome.

T1 seed were derived from self-pollination of each T0 event. The seedswere surface sterilized and germinated in vitro by sub-culturing thesterilized seeds on multiplication medium, as described previously.After 10 days of growth at 24° C. under a 16/8 (light/dark) hourphotoperiod, the roots of the germinated seedlings were removed and theseedlings were transferred onto rooting medium containing 200 nMIMAZAMOX® (imidazolinone). The seedlings were incubated for 2-3 weeksunder the same conditions and the presence or absence of root re-growthwas recorded. Leaf tissue harvested from each seedling was used for DNAextraction, and a PCR assay to test for the presence of the modifiedAHAS gene using primers AHAS_(—)3F1 and AHAS_(—)3R1 (SEQ ID NO:95 andSEQ ID NO:96) was completed, as described previously. Electrophoreticseparation of the resulting PCR products on agarose gel was used todetect the presence of the modified AHAS gene. The amplification of onlya 750-bp fragment PCR product indicated the absence of the modified AHASgene. Comparatively, the amplification of only a 850-bp fragmentindicated the presence of the modified AHAS gene in the homozygousstate. Furthermore, the amplification of both a 750-bp and 850-bpfragment indicated the presence of the modified AHAS gene in thehemizygous state.

Next, a chi-square test was used to confirm the inheritance of themodified AHAS gene as a single genetic unit. Expected Mendelianinheritance was observed in the T1 generation for each of the threewheat transformation events. The modified AHAS gene segregated at the3:1 ratio expected for a PCR test producing a dominant marker (Table 16)in the T1 seedlings. Similarly, IMAZAMOX® tolerance showed 3:1segregation, as expected for the dominant AHAS herbicide tolerancephenotype conferred by the S653N mutation (Table 17) in the T1seedlings.

TABLE 16 Segregation of modified AHAS gene in T1 seedlings derived fromself-pollination of transformed wheat plants from Example 5. No. of T1No. of T1 plants No. of plants with without T1 exogenous exogenousSegregation Event plants sequence sequence ratio tested P-valuemb1k-7783-1-1 25 19 6 3:1 p < 0.05 yr00-7794-1-1 54 44 10 3:1 p < 0.05yt02-7786-1-1 33 27 6 3:1 p < 0.05

TABLE 17 Segregation of IMAZAMOX ® tolerance phenotype in T1 seedlingsderived from self-pollination of transformed wheat plants from Example5. No. of T1 plants No. of No. of T1 without T1 plants IMI IMISegregation Event plants tolerance tolerance ratio tested P-valuemb1k-7783-1-1 25 19 6 3:1 p < 0.05 yr00-7794-1-1 54 44 10 3:1 p < 0.05yt02-7786-1-1 33 27 6 3:1 p < 0.05

The stability of expression of the modified AHAS gene was verified byits correspondence with the AHAS herbicide tolerance phenotype. Completeconcordance was observed between the presence of one or more copies ofthe modified AHAS gene and IMAZAMOX® tolerance.

Self-Pollination and Artificial Crossing to Recover Plants with SpecificCombinations of Precise Genome Modifications

Artificial crossing between wheat transformation events produced inExample 5 can be used to generate wheat plants that have the S653Nmutation on a specific sub-genome, on multiple sub-genomes, or on allthree sub-genomes.

To generate homozygous wheat plants having the S653N mutation on aspecific sub-genome, three wheat events from Example 5 were allowed toself-pollinate and produce T1 seed. The three events; mb1k-7783-1-1,yw06-7762-2-1 and yw06-7834-1-1 were selected to have hemizygous AHASgenome modifications on the A-genome, B-genome and D-genome,respectively. About 15 T1 seed from each event were germinated and grownunder glasshouse containment conditions to produce T2 seed. Leafmaterial harvested from each T1 plant was used for DNA extraction andPCR assays were completed to determine the zygosity of the modified AHASgene. This PCR zygosity test was designed to amplify a fragment fromeach of the three homoeologous copies of the endogenous AHAS gene withina region containing the binding site for ZFNs 29732 and 29730 (encodedon plasmid pDAB190350), and to include genomic nucleotide sequencevariation. Enough genomic nucleotide sequence variation was included todifferentiate between the AHAS homoeologs, such that the resultingamplicons could be unequivocally attributed (at the sequence level) tothe wheat sub-genome from which they were derived. The primer pairs weresynthesized with the Illumina™ SP1 and SP2 sequences at the 5′ end toprovide compatibility with Illumina™ sequencing-by-synthesis chemistry.The synthesized primers also contained a phosphorothioate linkage at thepenultimate 5′ and 3′ nucleotides. The 5′ phosphorothioate linkageafforded protection against exonuclease degradation of the Illumina™ SP1and SP2 sequences. Likewise, the 3′ phosphorothioate linkage improvedPCR specificity for amplification of the target AHAS sequences usingon-off PCR (Yang et al., (2005) Biochem. Biophys. Res. Commun., March 4:328(1):265-72). The sequences of the primer pairs are provided in Table18.

TABLE 18  Primer sequences used to assess thezygosity of the modified AHAS gene intransgenic wheat events from Example 5. SEQ ID Primer NamePrimer Sequence (5′→3′) NO: AHASs653ZFN.F2 a*cactctttccctacacgacg 297ctcttccgatctGCAATCA AGAAGATGCTTGAGAC*C AHASs653ZFN.R1g*tgactggagttcagacgtgt 298 gctcttccgatctTCTTTTG TAGGGATGTGCTGTCA*T Theasterisk(*) indicates a phosphorothioate; lowercase font indicates SP1and SP2 sequences, and uppercase font indicates the genomic DNAsequence.

The resulting PCR amplicons were prepared for deep sequencing asdescribed previously, and sequenced on an Illumina MiSEQ™ instrument togenerate 250-bp paired-end sequence reads, according to themanufacturer's instructions. The resultant sequence reads werecomputationally processed, as described previously, to assign each readto sample (based on the barcode index) and the sub-genome from whichthey were derived (based on nucleotide variation that distinguishedbetween homoeologous copies of the AHAS gene), and to perform qualityfiltering to ensure that only high quality sequences were used forsubsequent analyses. Custom developed PERL scripts and manual datamanipulation in MICROSOFT EXCEL 2010™ (Microsoft Corporation) were usedto process the data and determine the zygosity of the modified AHAS genein each T1 wheat event.

As the integration of pDAS000267 into the endogenous AHAS locus resultedin only a 95-bp size difference between the wild-type (unmodified) andresulting transgenic (modified) allele, the PCR zygosity assay wasexpected to amplify both the wild-type and modified AHAS gene.Consequently, T1 plants, homozygous for the target genome modification,were expected to produce only sequence reads that originate from theamplification of the transgenic allele at the modified AHAS locus. Thesealleles were distinguishable at the sequence level by the six mutationsdeliberately introduced into the AHAS exon in pDAS000267 (e.g., the twomutations encoding the S653N mutation, and the four codon-optimized,synonymous mutations positioned across the binding site of ZFN 29732prevented re-cleavage of the integrated donor). The T1 plants hemizygousfor the target genome modification were expected to produce sequencereads originating from both the wild-type and transgenic allele at themodified AHAS locus. Whereas, T1 plants without the modified AHAS genewere expected to only produce sequence reads originating from thewild-type allele at the modified AHAS locus. Based on the PCR zygositytest, T1 plants homozygous for the S653N mutation in only the A-genome,B-genome, or D-genome were identified (Table 19).

TABLE 19 PCR zygosity assay results for T1 plants derived fromself-pollination of transgenic wheat events from Example 5. A-genomeB-genome D-genome No. of No. of No. of No. of No. of No. of WT ED WT EDWT ED Event T1 plant reads¹ reads² reads reads reads reads Genotype³mb1k- mb1k- 39,305 46,481 92,167 2,011 85,048 2,222 AaBBDD 7783-17783-1-29 mb1k- mb1k- 95,696 61,451 203,228 3,913 200,232 4,087 AaBBDD7783-1 7783-1-31 mb1k- mb1k- 32,608 27,270 67,551 1,440 70,588 1,632AaBBDD 7783-1 7783-1-33 mb1k- mb1k- 37,172 56,416 76,005 1,693 77,8991,787 AaBBDD 7783-1 7783-1-39 mb1k- mb1k- 31,782 37,945 74,540 1,47876,916 1,892 AaBBDD 7783-1 7783-1-41 mb1k- mb1k- 3,784 93,125 189,5704,164 160,769 3,931 aaBBDD 7783-1 7783-1-43 mb1k- mb1k- 208,627 4,902241,948 4,567 247,912 5,094 AABBDD 7783-1 7783-1-46 mb1k- mb1k- 66,47239,215 134,076 2,464 126,823 2,613 AaBBDD 7783-1 7783-1-47 mb1k- mb1k-83,048 1,906 85,267 1,586 87,773 1,794 AABBDD 7783-1 7783-1-49 mb1k-mb1k- 41,810 34,455 81,446 1,603 82,871 1,776 AaBBDD 7783-1 7783-1-53mb1k- mb1k- 73,129 48,692 164,791 3,233 155,375 3,205 AaBBDD 7783-17783-1-55 mb1k- mb1k- 2,971 119,900 97,509 2,161 96,476 2,563 aaBBDD7783-1 7783-1-57 mb1k- mb1k- 2,076 60,517 62,638 1,444 59,721 1,827aaBBDD 7783-1 7783-1-58 mb1k- mb1k- 1,777 78,101 56,566 1,239 55,3021,326 aaBBDD 7783-1 7783-1-59 mb1k- mb1k- 64,093 57,599 135,703 2,713132,205 2,863 AaBBDD 7783-1 7783-1-61 yw06- yw06- 13,123 374 21,286 53221,471 560 AABBDD 7762-2 7762-2-23 yw06- yw06- 56,120 1,382 87,745 1,63582,753 2,170 AABBDD 7762-2 7762-2-24 yw06- yw06- 39,091 1,053 1,52538,594 61,284 1,578 AAbbDD 7762-2 7762-2-25 yw06- yw06- 24,551 804 1,42819,364 37,500 1,184 AAbbDD 7762-2 7762-2-27 yw06- yw06- 44,494 1,23432,935 18,811 64,736 1,733 AABbDD 7762-2 7762-2-28 yw06- yw06- 33,554964 22,898 11,718 45,887 1,221 AABbDD 7762-2 7762-2-29 yw06- yw06-33,410 1,011 1,481 26,659 46,214 1,430 AAbbDD 7762-2 7762-2-30 yw06-yw06- 56,639 1,516 44,649 17,155 85,830 2,116 AABbDD 7762-2 7762-2-31yw06- yw06- 45,753 1,223 35,723 13,649 69,858 1,781 AABbDD 7762-27762-2-32 yw06- yw06- 12,239 306 17,611 333 18,324 498 AABBDD 7762-27762-2-33 yw06- yw06- 38,709 1,001 32,109 14,549 61,150 1,620 AABbDD7762-2 7762-2-34 yw06- yw06- 48,185 1,329 40,719 16,138 75,876 1,953AABBDD 7762-2 7762-2-35 yw06- yw06- 44,420 1,096 71,463 1,374 72,6041,721 AABBDD 7762-2 7762-2-36 yw06- yw06- 23,752 685 37,126 796 36,283941 AABBDD 7762-2 7762-2-37 yw06- yw06- 43,467 1,092 68,043 1,317 65,7481,677 AABBDD 7834-1 7834-1-28 yw06- yw06- 47,463 1,177 72,531 1,39038,007 14,387 AABBDd 7834-1 7834-1-29 yw06- yw06- 51,138 1,484 77,2661,797 1,770 27,955 AABBdd 7834-1 7834-1-31 yw06- yw06- 42,666 1,33670,422 1,578 38,234 17,932 AABBDd 7834-1 7834-1-32 yw06- yw06- 33,075907 55,545 1,331 28,610 10,916 AABBDd 7834-1 7834-1-33 yw06- yw06-47,971 1,277 78,765 1,671 1,536 29,627 AABBdd 7834-1 7834-1-34 yw06-yw06- 44,355 1,043 74,365 1,347 68,161 1,634 AABBDD 7834-1 7834-1-35yw06- yw06- 67,661 1,788 93,068 2,329 2,214 31,935 AABBdd 7834-17834-1-36 yw06- yw06- 33,663 826 49,051 973 52,989 1,274 AABBDD 7834-17834-1-37 yw06- yw06- 45,974 1,080 67,706 1,258 67,774 1,619 AABBDD7834-1 7834-1-38 yw06- yw06- 2,687 27,436 88,976 2,084 92,612 2,892AABBDD 7834-1 7834-1-39 yw06- yw06- 62,142 1,713 93,532 2,233 49,88621,129 AABBDd 7834-1 7834-1-40 yw06- yw06- 50,781 1,381 77,168 1,69637,412 14,167 AABBDd 7834-1 7834-1-41 yw06- yw06- 44,020 1,233 61,2621,517 1,374 27,505 AABBdd 7834-1 7834-1-42 yw06- yw06- 68,958 1,45648,972 1,009 91,624 2,062 AABBDD 7834-1 7834-1-43 ¹Number of sequencereads originating from the specified sub-genome and having the sequencehaplotype corresponding to the wild-type (unmodified) AHAS locus. Theusage of “WT” indicates wild-type. ²Number of sequence reads originatingfrom the specified sub-genome and having the sequence haplotypecorresponding to the transgenic (modified) AHAS locus. The usage of “ED”indicates edited. ³Genotype for the T1 plant, where uppercase andlowercase letters indicate the presence of the wild-type and transgenicAHAS loci on the specified sub-genome, respectively. For example, AaBBDDindicates the T1 plant has a hemizygous AHAS genome modification on theA-genome and homozygous wild-type AHAS loci on the B- and D-genomes. Thezygosity at each of the three endogenous AHAS loci is determined fromthe frequency of the sequence reads corresponding to the wild-type andmodified alleles originating from each sub-genome. Hemizygous genotypeshave a similar frequency of wild-type and modified alleles originatingfrom an endogenous AHAS locus, where homozygous genotypes revealpredominantly wild-type or modified alleles. The low frequency ofalternate alleles originating from homozygous AHAS loci is due to PCRchimerism between reads originating from different sub-genomes.

One skilled in the art can deploy subsequent rounds of artificialcrossing between different wheat transformation events, in combinationwith the described PCR zygosity test, to produce homozygous wheat plantshaving the S653N mutation on any combination of multiple sub-genomes(e.g., the A-genome and B-genome, the A-genome and D-genome, or theB-genome and D-genome), or on all three sub-genomes. For example,artificial crossing of T1 plant mb1k-7783-1-43 (i.e., aaBBDD genotype)with T1 plant yw06-7762-2-25 (i.e., AAbbDD genotype) would produce T2seed that are hemizygous for modified AHAS genes in the A-genome andB-genomes; i.e., with the AaBbDD genotype. Subsequent, growth andself-pollination of T2 plants would produce T3 seed segregating forhomozygous genotypes for the modified AHAS genes on the A- and B-genomes(i.e., aabbDD genotype), which can be identified using the described PCRzygosity assay.

Example 10 Development of a Transformation System for Sequential,Exogenous Transgene Stacking at the Endogenous AHAS Loci in Wheat

The endogenous AHAS gene locus in wheat was selected as a model locus todevelop a ZFN-mediated, exogenous transformation system for generatingplants with one or more transgenes precisely positioned at the samegenomic location. The transformation system enables parallel(simultaneous integration of one or more transgenes) or sequentialstacking (consecutive integration of one or more transgenes) atprecisely the same genomic location. In addition, the transformationsystem includes simultaneous parallel or sequential stacking at multiplealleles across multiple sub-genomes. The strategies exploitincorporating mutations in the AHAS gene that confer tolerance to GroupB herbicides (e.g., ALS inhibitors such as imidazolinone orsulfonylurea).

ZFN-mediated integration of a donor DNA into the wild-type (herbicidesusceptible) AHAS locus was used to introduce transgene(s) and amutation to the endogenous AHAS gene that conferred tolerance toimidazolinones, thus allowing the regeneration of correctly targetedplants that possess tolerance to an imidazolinone selection agent.

Stacking of a second transgene(s) at the AHAS locus is achieved byintegration of a donor DNA that introduces one or more additionaltransgenes and confers susceptibility to imidazolinones, but toleranceto sulfonylureas, thus allowing the regeneration of correctly targetedplants using a sulfonylurea selection agent.

Stacking of a third transgene is achieved by integration of a donormolecule that introduces further transgene(s) and confers susceptibilityto sulfonylurea and tolerance to imidazolinones, thus allowing theregeneration of correctly targeted plants using an imidazolinoneselection agent.

As such, continued rounds of sequential transgene stacking are possibleby the use of donor DNA that introduce transgene(s) and mutations at theendogenous AHAS gene for differential cycling between imidazolinone andsulfonylurea selection agents. The transgenes can be integrated withinthe AHAS gene and stacked via an NHEJ and/or HDR pathway. The desiredrepair and recombination pathway can be determined by the design of thedonor transgene. In an embodiment, exogenous sequences that areintegrated and stacked within the AHAS gene would be designed to containa 5′ and 3′ region of homology to the genomic integration site; i.e. theAHAS gene. The 5′ and 3′ region of homology would flank the payload(e.g., AHAS mutation and gene of interest). Accordingly, such a designwould utilize an HDR pathway for the integration and stacking of thedonor polynucleotide within the chromosome. In a subsequent embodiment,transgenes that are integrated and stacked within the AHAS gene would bedesigned to contain single or double cut ZFN sites that flank thepayload (e.g., AHAS mutation and gene of interest). Accordingly, such adesign would utilize an NHEJ pathway for the integration and stacking ofthe donor polynucleotide within the chromosome.

Design and Production of Donor DNA for First Sequential TransgeneStacking at an Endogenous AHAS Locus Using NHEJ-Directed DNA Repair

The donor DNA for the first round of transgene stacking was designed topromote precise donor integration at an endogenous AHAS locus viaZFN-mediated, NHEJ-directed repair. The design was based on theintegration of a double stranded donor molecule at the position of thedouble strand DNA break created by cleavage of a homoeologous copy ofthe endogenous AHAS gene by ZFNs 29732 and 29730 (encoded on plasmidpDAB109350, FIG. 1).

The donor molecule backbone of pDAS000433 (SEQ ID NO:71; FIG. 12)comprised several polynucleotide sequence features. The 5′ end containedsequence that was nearly identical to the endogenous AHAS gene encodedin the D-genome. This sequence was made up of a fragment that spannedfrom the target ZFN cleavage site and finished at the AHAS stop codon.In addition, seven deliberate mutations were introduced into thesequence: the two mutations that encoded the S653N mutation and the fivecodon-optimized, synonymous mutations positioned across the binding siteof ZFN 29732. The five codon-optimised, synonymous mutations wereincluded to prevent re-cleavage of the integrated donor. Next, the stopcodon was followed by 316-bp of non-coding sequence corresponding to theconserved 3′ untranslated region (3′UTR) across the AHAS homoeologs. Inaddition, the 3′UTR sequence was followed by Zinc Finger binding sitesfor ZFNs 34480 and 34481 (encoded on plasmid pDAB111860) and ZFNs 34482and 34483 (encoded on plasmid pDAB111861). These Zinc Finger bindingsites allow for self-excision of donor-derived AHAS (coding and 3′UTR)sequence integrated at the endogenous locus during the second round oftransgene stacking. The self-excision Zinc Finger binding sites werefollowed by two additional Zinc Finger binding sites, which were flankedby 100-bp of random sequence. These two additional Zinc-Finger bindingsites were immediately followed by a pair of unique restrictionendonuclease cleavage sites that were used to insert the transgeneexpression cassette (i.e., the PAT expression cassette, as describedbelow). Following the two unique restriction endonuclease sites were twomore Zinc Finger binding sites, which were again flanked by 100-bp ofrandom sequence. The inclusion of the four additional Zinc Fingerbinding sites enable future excision of transgenes integrated at an AHASlocus by sequential marker-free transgene stacking, or continuedsequential transgene stacking at the same genomic location using analternate stacking method.

The donor backbone cassette was synthesized by a commercial gene servicevendor (GeneArt, Life Technologies) with a short stretch of additionalflanking sequence at the 5′ and 3′ ends to enable generation of a donormolecule with protruding 5′ and 3′ ends that were compatible with theligation overhangs generated by ZFNs 29732 and 29730 (encoded on plasmidpDAB109350) upon cleavage of an endogenous AHAS locus.

The PAT expression cassette was inserted, using standard methods knownto a person skilled in the art, into the donor backbone cassette ofpDAS000433 between the two unique restriction endonuclease sites toproduce the donor molecule cassette “QA_pDAS000434” (SEQ ID NO:314; FIG.19). The PAT selection cassette was comprised of the promoter, 5′untranslated region, and intron from the Actin (Act1) gene from Oryzasativa (McElroy et al., (1990) The Plant Cell, 2(2): 163-171) followedby a synthetic, plant-optimized version of phosphinothricin acetyltransferase (PAT) gene, isolated from Streptomyces viridochromogenes,which encodes a protein that confers resistance to inhibitors ofglutamine synthetase comprising phosphinothricin, glufosinate, andbialaphos (Wohlleben et al., (1988) Gene, 70(1): 25-37). This cassettewas terminated with the 3′ UTR comprising the transcriptional terminatorand polyadenylation sites from the 35s gene of cauliflower mosaic virus(CaMV) (Chenault et al., (1993) Plant Physiology 101 (4): 1395-1396).Plasmid DNA for “QA_pDAS000434” was prepared using the PURE YIELDPLASMID MAXIPREP SYSTEM™ (Promega Corporation, WI) following themanufacturer's instructions.

PCR amplification of “QA_pDAS000434” followed by digestion withrestriction endonuclease BbsI was used to produce linear double-strandedDNA donor molecules with protruding 5′ and 3′ ends that were compatiblewith the ligation overhangs generated by ZFNs 29732 and 29730 (encodedon plasmid pDAB109350) upon cleavage of an endogenous AHAS locus. PCRamplification was performed with primers AHAS_TSdnr1_F1 andAHAS_TSdnr1_R1 (SEQ ID NO: 297 and 298, respectively), which weredesigned to the short stretch of additional sequence added to the 5′ and3′ ends of the donor backbone cassette “QA_pDAS000434”. The resultingamplicons were purified using the Agencourt AMPure™ XP-PCR purificationkit (Beckman Coulter) and digested with BbsI (New England Biolabs). Theamplicons were purified a second time using the Agencourt AMPure™ XP-PCRpurification kit (Beckman Coulter), followed by ethanol precipitationand resuspension in sterile water at a DNA concentration appropriate forwheat transformation. Standard methods known to a person skilled in theart were used to prepare the linear double-stranded DNA donor molecule.

Production of Control Binary Vector Encoding AHAS (S653N)

A binary vector pDAS000143 (SEQ ID NO:88, FIG. 10) containing AHAS(S653N) expression and PAT selection cassettes was designed andassembled using skills and techniques commonly known in the art aspreviously described. Plasmid DNA for the binary was prepared using thePURE YIELD PLASMID MAXIPREP SYSTEM™ (Promega Corporation, WI) followingthe manufacturer's instructions. The binary vector pDAS000143 wastransformed into wheat cells as a control.

Biolistics-Mediated Transformation for Generating Wheat Events withFirst Sequential Transgene Stack at an Endogenous AHAS Locus UsingNHEJ-Directed DNA Repair

A total of 55,468 scutella of immature zygotic embryos from the donorwheat line cv. Bobwhite MPB26RH were prepared for biolistics-mediatedDNA delivery, as described previously. DNA-coated gold particles wereprepared with the formulations as described above. For transfectionsperformed using the linear double-stranded donor DNA derived from“QA_pDAS000434” or pDAS000433, the donor DNA was mixed at a 5:1 molarratio with plasmid DNA for pDAB109350 (encoding ZFNs 29732 and 29730).Transfections performed using pDAS000143 were performed using goldparticles that were coated only with plasmid DNA for pDAS000143.

Biolistic-mediated transfections were performed as described previously.Following bombardment, the transfected scutella were incubated at 26° C.in the dark for 16 h before being transferred onto medium for callusinduction.

Two different chemical selection strategies were used to enrich forregenerated wheat plants with an integrated linear double-stranded donormolecule. The first strategy based on IMAZAMOX® was used to recoverwheat events that had the donor molecule precisely integrated into oneor more homoeologous copies of the endogenous AHAS gene by ZFN-mediatedNHEJ-directed gene editing. Such events are expected to have the AHASherbicide tolerance phenotype conferred by the S653N mutation. Thesecond strategy based on BASTA® (DL-Phosphinothricin) was used torecover events that had the donor molecule integrated at either a random(non-targeted) position in the wheat genome, or imperfectly integratedinto one or more homoeologous copies of the endogenous AHAS gene byZFN-mediated NHEJ-directed gene editing. These events are expected toexhibit the BASTA® herbicide tolerance phenotype conferred by the PATgene, but not necessarily the AHAS herbicide tolerance phenotypeconferred by the S653N mutation. The purpose of the second chemicalselection strategy was to allow the frequency of precise (on-target)versus random (off-target) donor integration to be quantified, as wellas the frequency of perfect and imperfect integration at the endogenousAHAS loci. The two chemical selection strategies are described in Table20.

TABLE 20 Chemical selection strategies used to regenerate wheat plantsthat had an integrated donor molecule Plant Regeneration Stage IMISelection PPT Selection Callus Induction (CIM) 150 nM None PlantRegeneration (DRM) 150 nM 5 mg/ml PPT Rooting (RM) 200 nM 5 mg/ml PPT(“IMI” indicates IMAZAMOX ® and “PPT” Indicates BASTA ® selection).

A total of 34,546 and 23,550 transfected scutella were subject toIMAZAMOX® and BASTA® selection, respectively. For each strategy,scutella were cultured in the dark on callus induction medium at 24° C.for 2 weeks. The resultant calli were sub-cultured once onto freshcallus induction medium and kept in the same conditions for a furthertwo weeks. Somatic embryogenic callus (SEC) were transferred onto plantregeneration medium and cultured for 2 weeks at 24° C. under a 16/8(light/dark) hour photoperiod in a growth room. Regenerated plantletswere transferred onto rooting medium and cultured under the sameconditions for 2-3 weeks. For IMAZAMOX® selection, the regeneratedplants were sub-cultured for a total of three times on rooting media. Atthe end of each round, the roots of regenerated plants were removed andthe plants were again sub-cultured on rooting media under the sameconditions. Plantlets with roots were transferred to soil and grownunder glasshouse containment conditions. T₁ seed was harvested fromindividual plants, following bagging of individual spikes to preventout-crossing.

The scutella explants bombarded with gold particles coated withpDAS000143 were used to monitor the selection stringency across both theIMAZAMOX® and BASTA® chemical selection strategies. Plants transformedwith pDAS000143 were regenerated using the process described above.

A total of 36 wheat plants were recovered from each chemical selectionstrategy for scutella explants transfected with pDAS000143. Moleculartesting of these events using the hydrolysis probe assay described inExample 6 confirmed that all of the recovered wheat plants carried atleast one randomly integrated copy of the pDAS000143 insert. Theseresults indicated that the IMAZAMOX® and BASTA® selection conditionswere sufficiently stringent to ensure a low escape rate (i.e., recoveryof wheat plants that were not transformed), whilst allowing the recoveryof events carrying one or more integrated copies of the AHAS (S653N) andPAT donor polynucleotides, respectively.

No wheat plants having the AHAS herbicide tolerance phenotype conferredby the S653N mutation were recovered from IMAZAMOX® selection under thespecific selection conditions described above. As IMAZAMOX® selection isexpected only to recover wheat plants that have precise integration ofthe donor molecule into one or more copies of the homoeologous AHASgene, these results suggest that the chemical selection regime wassub-optimal, and that the conditions should be modified for preciseZFN-mediated NHEJ-directed integration of pDAS000433 donor at anendogenous AHAS locus, or that the scale of transformation was notappropriate for the chemical selection conditions used in the currentwork. In contrast, 1,652 wheat plants were recovered from BASTA®selection. As BASTA® is expected to recover wheat plants that have bothtargeted and non-targeted (random) donor integration, molecularcharacterization of these events can distinguish between targeted andnon-targeted donor integration, which can provide guidance for refiningIMAZAMOX® selection conditions.

Molecular Characterisation of BASTA®-Selected Wheat Plants for Evidenceof First Transgene Stacking at an Endogenous AHAS Locus

A total of 1,162 wheat plants recovered from BASTA®-selection weremolecularly characterized to assess the frequency of targeted andoff-target (random) donor integration, as well as the frequency oftargeted perfect and imperfect donor integration at the endogenous AHASloci.

Three molecular assays were performed for each wheat plant using genomicDNA extracted with the DNEASY® PLANT DNA EXTRACTION MINI KIT™ (Qiagen)from freeze-dried leaf tissue, as described previously.

The first molecular test was used to confirm that the regenerated wheatplants carried at least one integrated copy of the linear double-strandDNA derived from “QA_pDAS000434”. This test involved a PCR assay toamplify a region of the Actin (Act1) promoter present in “QA_pDAS000434”(SEQ ID NOs: 92 and 93 for forward and reverse primers, respectively),followed by electrophoretic separation of the resulting amplicon on anagarose gel. The presence of a PCR fragment of expected size (218-bp)indicated integration of at least one copy of the donor molecule. Of the1,162 wheat events, 1,065 (92%) produced a PCR fragment of the expectedsize.

The second molecular test was used to identify wheat plants having thedonor molecule putatively integrated into one or more copies of theendogenous AHAS locus. This test comprised an on-off PCR assay using aprimer designed to hybridize to a region upstream of the binding sitefor ZFNs 29732 and 29730 (encoded on plasmid pDAB190350) in each of thehomoeologous copies of the endogenous AHAS gene, and a primer designedto hybridize to a region within the 100-bp of random sequence flankingthe binding site for ZFNs 34480 and 34481 (encoded on plasmidpDAB111860) in “QA_pDAS000434” (SEQ ID NO: 299 and 300 for forward andreverse primers, respectively). Each primer was designed with aphosphorothioate linkage positioned at the penultimate base to maximizespecificity for primer extension during PCR amplification. Amplificationof a PCR fragment with size greater than 300-bp when separated byelectrophoresis on agarose gel was considered as suggestive evidence fortargeted integration (of least a portion) of the donor molecule into oneor more copies of the endogenous AHAS gene. Of the 1,065 wheat eventstested, 543 (51%) amplified a PCR fragment of greater than 300-bp insize.

The third molecular assay was used to further characterize wheat plantsshowing suggestive evidence for targeted integration of the donormolecule in one or more copies of the endogenous AHAS gene. This testinvolved a PCR assay using a pair of primers designed to amplify a256-bp region from the three homoeologous copies of the endogenous AHASgene. This region contained the binding site for ZFNs 29732 and 29730(encoded on plasmid pDAB190350), and to include genomic nucleotidesequence variation. Enough genomic nucleotide sequence variation wasincluded to differentiate between the AHAS homoeologs, such that theresulting amplicons could be unequivocally attributed (at the sequencelevel) to the wheat sub-genome from which they were derived. The primerpairs were synthesized with the Illumina™ SP1 and SP2 sequences at the5′ end, respectively, to provide compatibility with Illumina™sequencing-by-synthesis chemistry. The synthesized primers alsocontained a phosphorothioate linkage at the penultimate 5′ and 3′nucleotides. The 5′ phosphorothioate linkage afforded protection againstexonuclease degradation of the Illumina™ SP1 and SP2 sequences, whilethe 3′ phosphorothioate linkage improved PCR specificity foramplification of the target AHAS sequences using on-off PCR. Thesesequences of the primer pair are given in Table 21.

TABLE 21  Primer sequences used to further characterizewheat plants having suggestive evidence fortargeted integration of the donor molecule inone or more copies of the endogenous AHAS gene. SEQ ID Primer NamePrimer Sequence (5′→3′) NO: AHASs653ZFN.F2 a*cactctttccctacacgacg 301ctcttccgatctGCAATCA AGAAGATGCTTGAGAC*C AHASs653ZFN.R3g*tgactggagttcagacgtgt 302 gctcttccgatctCAAGCA AACTAGAAAACGCATG*G Theasterisk(*) indicates a phosphorothioate; lowercase font indicates SP1and SP2 sequences, and upper case font indicates the genomic DNAsequence.

PCR amplicons produced by the third molecular assay were prepared fordeep sequencing by performing an additional round of PCR to introducethe Illumina™ P5 and P7 sequences onto the amplified DNA fragments, aswell as a sequence barcode index that could be used to unequivocallyattribute sequence reads to the sample from which they originated. Thiswas achieved using primers that were in part complementary to the SP1and SP2 sequences added in the first round of amplification, but alsocontained the sample index and P5 and P7 sequences. Followingamplification, the generated products were sequenced on an IlluminaMiSEQ™ instrument to generate 250-bp paired-end sequence reads,according to the manufacturer's instructions.

The resultant paired-end 250-bp sequence reads were computationallyprocessed, as described previously, to assign each read to sample (basedon the barcode index) and the sub-genome from which they were derived(based on nucleotide variation that distinguished between homoeologouscopies of the AHAS gene), and to perform quality filtering to ensurethat only high quality sequences were used for subsequent analyses.Custom developed PERL scripts and manual data manipulation in MICROSOFTEXCEL 2010™ (Microsoft Corporation) were used, as described below, toidentify reads that contained evidence for targeted integration of thedonor into one or more copies of the endogenous AHAS gene.

As the hybridization site for primer AHASs653ZFN.R3 (Table 21) was alsopresent in the AHAS 3′ untranslated region (UTR) in “QA_pDAS000434”, thethird molecular assay allowed for differentiation between targeted andrandom donor integration, as well as between perfect and imperfect donorintegration at one or more copies of the endogenous AHAS locus. Wheatplants having perfect hemizygous on-target editing are expected toproduce sequence reads that originate from amplification of both thewild-type (unedited) and edited alleles at each modified AHAS locus.These alleles are distinguishable at the sequence level by the sevendeliberate mutations introduced into the AHAS exon in “QA_pDAS000434”(i.e., the two mutations encoding the S653N mutation and the fivecodon-optimized, synonymous mutations positioned across the binding siteof ZFN 29732, which were incorporated to prevent re-cleavage of theintegrated donor). Theoretically, the frequency of reads correspondingto the wild-type and edited alleles should occur at a ratio of 1:1 foreach endogenous AHAS locus with perfect hemizygous editing. In contrast,wheat plants having perfect homozygous on-target editing are expected toonly generate sequence reads that originate from the pair of editedalleles at each modified endogenous AHAS locus. As the primer pair usedin the third molecular assay were designed to amplify all threehomoeologous copies of the AHAS gene, the expected generation of readsoriginating from all three wheat sub-genomes can also be used to detecton-target imperfect donor integration (e.g., integration of a partialdonor fragment, or integration of the donor fragment in the wrongorientation). Imperfect on-target donor integration is expected toresult in amplification of only the wild-type (unedited) allele fromeach modified endogenous AHAS locus due to PCR competition favoring theamplification of the shorter wild-type fragment. Consequently,hemizygous on-target imperfect donor integration is expected to generateabout half as many reads originating from the sub-genome into whichintegration occurred, compared to unedited sub-genomes. For homozygouson-target imperfect donor integration, no reads are expected tooriginate from the sub-genome into which integration occurred.Conversely, off-target (random) donor integration is expected togenerate an equal proportion of sequence reads originating from allthree homoeologous copies of the AHAS gene.

Sequence analysis of the 543 wheat plants tested revealed 38 events withmolecular evidence for on-target donor integration in one or more copiesof the endogenous AHAS gene. Event di01-9632-1-1 had perfect hemizygousdonor integration in the AHAS locus situated in the B-genome. Theseresults were indicated by the presence of both wild-type and perfectlyedited reads originating from the B-genome, and only wild-type allelesoriginating from the A- and D-genome (Table 22). Two events hadimperfect hemizygous donor integration in the AHAS loci on the A- andD-genomes, respectively. Event yl02-9453-1-2 had both wild-type andimperfectly edited reads originating from the D-genome, and onlywild-type alleles originating from the A- and B-genomes. Comparatively,event yl02-9552-21-1 had both wild-type and imperfectly edited readsoriginating from the A-genome, and only wild-type alleles originatingfrom the other sub-genomes.

The remaining 35 events showed molecular evidence for imperfect donorintegration into at least one copy of the endogenous AHAS gene, wherethe donor molecule was likely to be truncated or integrated in the wrongorientation (Table 22). These events were characterized by a lower thanexpected frequency of reads originating from one or more of the wheatsub-genomes. For example, event yl02-9552-7-1 had a statisticallysignificant lower frequency of wild-type AHAS reads originating from theB-genome than expected for an unedited locus. The remaining 453 eventsshowed only evidence for random integration of the donor elsewhere inthe wheat genome, indicating that the amplified product from the secondmolecular assay most likely arose from PCR chimerism. The consensussequences for the edited alleles present in the B, D and A sub-genome ofwheat events di01-9632-1-1, yl02-9453-1-2 and yl02-9552-21-1 areprovided as SEQ ID NOs:303, 304 and 305, respectively.

TABLE 22 Molecular evidence for integration of QA_pDAS000434 into one ormore homoeologous copies of the endogenous AHAS locus. No. of Eventreads % Reads % WT % PE % IE A-genome di01-9632-1-1 17,312  9 99 0 1yl02-9453-1-2 8,548 20 97 3 0 yl02-9552-21-1 3,049 10 47 0 53yl02-9552-7-1 43,845 66 100 0 0 gt19-9595-10-1 48,681 62 100 0 0yr00-9553-3-1 16,212 16 98 1 0 yr00-9580-9-1 69,153 35 97 2 1yl02-9532-1-1 85,431 43 100 0 0 yl02-9532-16-1 14,318 29 100 0 0di01-9603-10-1 825  1* 100 0 0 yl02-9578-1-1 1,662  1* 100 0 0di01-9603-2-1 833  5* 100 0 0 yc06-9547-1-1 831  1* 100 0 0yl02-9532-9-1 2,168  1* 100 0 0 yc06-9522-1-1 4,233  2* 100 0 0mb1k-9539-31-1 2,355  2* 100 0 0 yl02-9503-1-1 1,381  1* 100 0 0mb1k-9546-4-1 1,971  2* 100 0 0 di01-9603-18-1 1,436  1* 100 0 0di01-9603-25-1 819  1* 100 0 0 yl02-9503-2-1 1,241  1* 100 0 0di01-9550-14-1 2,846  2* 100 0 0 yr00-9580-28-1 708  0* 100 0 0yl02-9552-19-1 4,127  2* 100 0 0 hw12-9569-5-1 1,959  1* 100 0 0gt19-9582-2-1 244  0* 99 0 1 gt19-9593-6-1 9,426  7* 100 0 0mb1k-9539-25-1 982  1* 100 0 0 yl02-9457-7-1 467  0* 100 0 0yr00-9553-16-1 433  0* 100 0 0 yw06-9345-15-1 146  4* 100 0 0mb1k-9546-2-1 93,058 97 99 0 1 yr00-9541-5-1 131,675 93 100 0 0yl02-9552-47-1 180,989 97 100 0 0 gt19-9551-4-1 144,978 99 100 0 0yc06-9340-5-1 96,105 98 100 0 0 yc06-9584-2-1 98,385 98 100 0 0yr00-9541-1-1 115,671 98 100 0 0 B-genome di01-9632-1-1 9,498  5 70 29 1yl02-9453-1-2 13,374 32 97 3 0 yl02-9552-21-1 16,817 55 100 0 0yl02-9552-7-1 6,254  9* 100 0 0 gt19-9595-10-1 5,146  7* 100 0 0yr00-9553-3-1 8,683  8* 100 0 0 yr00-9580-9-1 1,768  1* 98 1 1yl02-9532-1-1 6,644  3* 100 0 0 yl02-9532-16-1 34,310 70 100 0 0di01-9603-10-1 3,228  4* 100 0 0 yl02-9578-1-1 2,176  1* 100 0 0di01-9603-2-1 1,225  7* 100 0 0 yc06-9547-1-1 723  1* 100 0 0yl02-9532-9-1 1,012  0* 100 0 0 yc06-9522-1-1 3,979  2* 100 0 0mb1k-9539-31-1 2,359  2* 100 0 0 yl02-9503-1-1 601  0* 100 0 0mb1k-9546-4-1 364  0* 100 0 0 di01-9603-18-1 106,322 96 100 0 0di01-9603-25-1 101,834 98 100 0 0 yl02-9503-2-1 221,040 99 100 0 0di01-9550-14-1 130,434 96 100 0 0 yr00-9580-28-1 174,074 99 100 0 0yl02-9552-19-1 174,186 95 100 0 0 hw12-9569-5-1 260,971 98 100 0 0gt19-9582-2-1 67,764 99 100 0 0 gt19-9593-6-1 110,669 84 100 0 0mb1k-9539-25-1 75,915 96 100 0 0 yl02-9457-7-1 125,465 99 100 0 0yr00-9553-16-1 111,825 99 100 0 0 yw06-9345-15-1 3,655 93 100 0 0mb1k-9546-2-1 1,448  2* 100 0 0 yr00-9541-5-1 4,403  3* 100 0 0yl02-9552-47-1 2,236  1* 100 0 0 gt19-9551-4-1 740  1* 100 0 0yc06-9340-5-1 620  1* 100 0 0 yc06-9584-2-1 617  1* 100 0 0yr00-9541-1-1 781  1* 100 0 0 D-genome di01-9632-1-1 170,321 86 99 0 1yl02-9453-1-2 19,841 48 68 32 0 yl02-9552-21-1 10,665 35 100 0 0yl02-9552-7-1 15,936 24 100 0 0 gt19-9595-10-1 24,091 31 100 0 0yr00-9553-3-1 79,529 76 98 1 0 yr00-9580-9-1 128,317 64 97 2 1yl02-9532-1-1 105,821 53 100 0 0 yl02-9532-16-1 434  1* 99 1 0di01-9603-10-1 84,718 95 100 0 0 yl02-9578-1-1 152,767 98 100 0 0di01-9603-2-1 14,671 88 100 0 0 yc06-9547-1-1 71,423 98 100 0 0yl02-9532-9-1 230,632 99 100 0 0 yc06-9522-1-1 167,492 95 100 0 0mb1k-9539-31-1 142,061 97 100 0 0 yl02-9503-1-1 199,717 99 100 0 0mb1k-9546-4-1 89,309 97 100 0 0 di01-9603-18-1 2,921  3* 100 0 0di01-9603-25-1 1,715  2* 96 0 4 yl02-9503-2-1 1,741  1* 100 0 0di01-9550-14-1 3,140  2* 100 0 0 yr00-9580-28-1 1,012  1* 100 0 0yl02-9552-19-1 5,470  3* 100 0 0 hw12-9569-5-1 2,479  1* 100 0 0gt19-9582-2-1 496  1* 99 0 1 gt19-9593-6-1 11,821  9* 100 0 0mb1k-9539-25-1 1,898  2* 100 0 0 yl02-9457-7-1 555  0* 100 0 0yr00-9553-16-1 604  1* 100 0 0 yw06-9345-15-1 150  4* 100 0 0mb1k-9546-2-1 1,191  1* 100 0 0 yr00-9541-5-1 4,766  3* 100 0 0yl02-9552-47-1 3,537  2* 100 0 0 gt19-9551-4-1 1,171  1* 99 0 0yc06-9340-5-1 1,186  1* 100 0 0 yc06-9584-2-1 1,234  1* 100 0 0yr00-9541-1-1 1,566  1* 100 0 0 “No. of reads” indicates the number ofsequence reads assigned to the wheat sub-genome; “% Reads” indicates thepercentage of sequence reads assigned to the wheat sub-genome as aproportion of all assigned reads; “% WT” indicates the percentage ofsequence reads identified as wild type (unedited) alleles; “% PE”indicates the percentage of sequence reads indicating precise donorintegration into the wheat sub-genome; “% IE” indicates the percentageof sequence reads indicating imperfect donor integration into the wheatsub-genome; Asterisks(*) indicate occurrence of statisticallysignificant fewer sequence reads than expected for an uneditedendogenous AHAS locus

Overall, 3% (38/1,162) of the BASTA®-selected wheat events showedmolecular evidence for targeted donor integration into one or more ofthe homoeologous copies of the endogenous AHAS gene.

Example 11 Development of a Transformation System for Sequential,Exogenous Marker-Free Transgene Stacking at the Endogenous AHAS Loci inWheat

Wheat plants containing a donor integrated polynucleotide within theAHAS locus to introduce the S653N mutation are produced via thepreviously described methods. For example, the regeneration of eventdi01-9632-1-1 (Table 23) showing molecular evidence of perfecthemizygous integration of “QA_pDAS000434” in the B-genome of wheatindicates that donor DNA and zinc finger nuclease constructs can beutilized for the integration of donor molecule sequences at one or morecopies of the target endogenous AHAS locus within wheat. Producing suchan event, that is free of any additional transgenic selectable markers,is the initiating act for sequential, exogenous transgenic selectablemarker-free stacking of a donor polynucleotide at an endogenous AHASlocus in the genome of wheat. The edited plant events are obtained viaalternative selection conditions as previously described in Example 10.

The previously described selection conditions can be modified by anumber of methodologies. Other approaches can be implemented to enhancethe recovery of wheat plants with precise integration of the S653Nmutation (as encoded on “QA_pDAS000434” or pDAS000433) into one or morecopies of the endogenous AHAS locus, without using a transgenicselectable marker.

Two additional approaches can be implemented to enhance the recovery ofwheat plants with precise integration of the S653N mutation into one ormore copies of the endogenous AHAS locus, without the usage of atransgenic selectable marker.

For example, IMAZAMOX® selection conditions are modified, to includeselection at differing stages of culturing and/or lower concentrationsof the herbicide. Accordingly, selection at the plant regeneration stageis reduced by lowering the concentration of IMAZAMOX® added to the plantregeneration media or as another alternative the usage of herbicide atthis plant regeneration stage is completely eliminated. As such,stronger growth of regenerated plantlets is observed, thereby ensuringlarger plantlets that are less susceptible to tissue damage whensub-cultured to rooting media. Furthermore, the plantlets may berequired to be dissected from the embryogenic callus from which theyoriginate. Smaller plantlets are more susceptible to tissue damage,which can result in tissue necrosis and potential loss of transformedplantlets during sub-culturing. Maintenance of IMAZAMOX® selection atthe callus induction stage helps to restrict embryogenesis fromuntransformed cells, while its maintenance at the rooting stage wouldprovide strong selection for plantlets with precise integration ofpDAS000433 at one or more copies of the endogenous AHAS locus, which isrequired to produce the AHAS herbicide tolerance phenotypes conferred bythe S653N mutation. The success of such IMAZAMOX® selection strategiesfor generating precisely edited wheat plants was demonstrated in Example5.

In another example, a different transformation system is used togenerate wheat plants with precisely integrated donor DNA. For example,protoplast-based transformation could be used to produce individualcalli, where each callus is derived from a single cell.Protoplast-derived calli provide several advantages over callus derivedfrom biolistic-bombarded scutella of immature zygotic embryos. Unlikecallus derived from biolistics-bombardment, and which is chimeric forboth transformed and untransformed cells, protoplast-derived callus isclonal. Hence, cell survival in callus derived from a transformedprotoplast in which precise pDAS000433 integration has occurred cannotbe compromised by the presence of neighboring untransformed cells whensubject to IMAZAMOX® selection. In the case of callus derived frombiolistics-bombardment, the chimeric composition of the callus meansthat the survival of a precisely transformed can be compromised by thedeath of surrounding untransformed cells when subjected to IMAZAMOX®selection. Protoplast-based transformation systems also provide theadvantage of scalability, compared to biolistics bombardment, since manymore cells can be transformed for an given amount of effort, therebyproviding for higher probability for recovering wheat plants withprecise integration of pDAS000433 in one or more copies of theendogenous AHAS gene. Several protoplast-based transformation systemsfor wheat have been described in published scientific literature (Qiaoet al. (1992) Plant Cell Reports 11:262-265; Ahmed and Sagi (1993) PlantCell Reports 12:175-179; Pauk et al. (1994) Plant Cell, Tissue and OrganCulture 38: 1-10; He et al. (1994) Plant Cell Reports 14: 92-196; Gu andLang (1997) Plant Cell, Tissue and Organ Culture 50: 139-145; and Li etal. (1999) Plant Cell, Tissue and Organ Culture 58: 119-125).

A series of experiments are performed to determine optimal selectionconditions for regenerating wheat plants expressing the AHAS (S653N)mutation conferring tolerance to IMAZAMOX® from a protoplast-basedtransformation system such as those described above.

IMAZAMOX® selection conditions are optimized using protoplasts derivedfrom somatic embryogenic callus (SEC)-derived cell suspension culture ofthe wheat line cv. Bobwhite MPB26RH. While protoplasts derived fromBobwhite MPB26RH are non-totipotent (i.e., cannot be used to regenerateentire plants), the selection conditions established for enriching forevents expressing the AHAS (653N) mutation are expected to betransferable to any protoplast-based transformation system based on atotipotent wheat genotype, which those in the art would recognize. Theexperiments conducted establish the basal tolerance of the wild-typedonor wheat line cv. Bobwhite MPB26RH (S653/S653 genotype, which conferssusceptibility to imidazolinones) to IMAZAMOX®. The use of IMAZAMOX®selection conditions stronger than basal tolerance will strongly enrichfor transformed cells expressing the AHAS (S653N) mutation.

Further transformation methods are applicable. For example a cellsuspension culture for wheat line cv. Bobwhite MPB26RH can beestablished. Somatic embryogenic callus (SEC) is induced from immaturezygotic embryos of wheat line cv. Bobwhite MPB26RH as describedpreviously. A fast growing callus line is selected after six cycles ofsub-culturing on callus induction media. For each cycle ofsub-culturing, the fast-growing calli are transferred onto new callusinduction media and cultured in the dark at 26° C. for 14 d.

A cell suspension culture is initiated by transferring 1 gram calli ofthe fast-growing callus line to a flask containing 20 ml liquid growthmedium and culturing at 25° C. in the dark on a gyratory shaker at 90rpm. Every seven days the cell suspension culture is sub-cultured bypassing the culture through a fine gauze to remove cell clumps greaterthan 2 mm in diameter, and replacing two thirds of the culture mediawith fresh medium. After 3 months of repeated filtration andsub-culturing a fast-growing SEC-derived cell suspension culture isestablished.

Next protoplasts are isolated from the SEC-derived cell suspensionculture. About 4 grams fresh weight of cell clumps are obtained bypassing 7 day old SEC-derived cell suspension culture through afine-mesh. The cell clumps are digested in wheat callus digest mix, asdescribed previously, to release the protoplasts. The yield ofSEC-derived cell suspension culture protoplasts is estimated using aNeubauer™ haemocytometer. Evans Blue stain is used to determine theproportion of live cells recovered.

The protoplast culture selection conditions with the herbicide IMAZAMOX®are selected. An agarose bead-type culture system is used for protoplastculture. About 1×10⁶ protoplasts are precipitated by gentlecentrifugation and the supernatant is removed. The protoplasts areresuspended by gentle agitation in 1 ml of melted 1.2% Sea-Plaque™agarose cooled to 40° C. and transferred to a 3.5 cm petri dish.Following agarose solidification, 1 ml culture medium is added to thepetri dish and the plate is incubated at 25° C. in the dark for 1 week.The agarose plug is transferred into a 20 cm petri dish containing 10 mlculture medium and incubated at 25° C. in the dark on a gyratory shakerat 90 rpm. Every 14 days the culture medium is replaced with freshmedia. Protoplast cell division is typically observed 3 days afterembedding in agarose, with clumps of multiple cells visible after 7days.

The basal tolerance of wheat line cv. Bobwhite MPB26RH to IMAZAMOX® isdetermined by incubating the agarose bead-type cultures in mediasupplemented with 0, 50, 100, 200, 400 and 600 nM IMAZAMOX® andassessing the rate of calli growth after 2 weeks. IMAZAMOX®concentrations higher than 200 nM impede calli development, indicatingthat concentrations of 200 nM and higher are optimal for enriching andselecting wheat cells having the AHAS (S653N) mutation.

Establishment of tissue culture selection conditions for obtainingtransgenic plants with a donor integrated fragment resulting in theS653N mutation within the AHAS locus are obtained. The edited plantevents are used to generate explant material (e.g., protoplasts orscutella of immature zygotic embryos) for a second round oftransfection. As described in the next example, the explant material issubsequently co-transfected with a donor DNA molecule and a plasmidencoding a ZFN that is designed to target a Zinc Finger binding sitelocated in the AHAS genes upstream of the region encoding the P197 aminoacid residue.

Example 12 Alternate Transformation Systems for Sequential, ExogenousMarker-Free Transgene Stacking at the Endogenous AHAS Loci in Wheat

Molecular evidence provided in Example 10 for the regenerated wheatplant event di01-9632-1-1 demonstrates the technical feasibility forsequential, exogenous marker-free transgene stacking at the endogenousAHAS loci in wheat. Refinement of IMAZAMOX® selection conditions or useof a different transformation system permit the production of wheatplants with sequentially stacked transgenes at an endogenous AHAS locus.This example describes approaches for achieving exogenous marker-freesequential transgene stacking at an endogenous AHAS locus by alternatingbetween different selective agents (e.g., imidazolinone andsulfonylurea) and corresponding AHAS mutations (e.g., S653N and P197S).First, the selection conditions for sulfonylurea were determined.

Optimization of Chemical Selection Conditions; Generation of Low-Copy,Randomly Integrated T-DNA Wheat Plants with AHAS (P197S) ExpressionConstructs

A binary vector pDAS000164 (SEQ ID NO:289, FIG. 11) containing AHAS(P197S) expression and PAT selection cassettes was designed andassembled using skills and techniques commonly known in the art. TheAHAS (P197S) expression cassette consisted of the promoter, 5′untranslated region, and intron from the Ubiquitin (Ubi) gene from Zeamays (Toki et al., (1992) Plant Physiology, 100: 1503-07) followed bythe coding sequence (1,935 bp) of the AHAS gene from T. aestivum cv.Bobwhite MPB26RH with nucleotide 511 mutated from C to T in order toinduce an amino acid change from proline (P) to serine (S). The AHASexpression cassette included the 3′ untranslated region (UTR) comprisingthe transcriptional terminator and polyadenylation site of the nopalinesynthase gene (nos) from A. tumefaciens pTi15955 (Fraley et al., (1983)Proceedings of the National Academy of Sciences U.S.A., 80(15):4803-4807). The selection cassette was comprised of the promoter, 5′untranslated region, and intron from the Actin (Act1) gene from Oryzasativa (McElroy et al., (1990) The Plant Cell 2(2): 163-171) followed bya synthetic, plant-optimized version of phosphinothricin acetyltransferase (PAT) gene, isolated from Streptomyces viridochromogenes,which encodes a protein that confers resistance to inhibitors ofglutamine synthetase comprising phosphinothricin, glufosinate, andbialaphos (Wohlleben et al., (1988) Gene, 70(1): 25-37). This cassettewas terminated with the 3′ UTR comprising the transcriptional terminatorand polyadenylation sites from the 35s gene of the cauliflower mosaicvirus (CaMV) (Chenault et al., (1993) Plant Physiology, 101 (4):1395-1396).

The selection cassette was synthesized by a commercial gene synthesisvendor (e.g., GeneArt, Life Technologies, etc.) and cloned into aGATEWAY®-enabled binary vector with the RfA Gateway cassette locatedbetween the Ubiquitin (Ubi) gene from Zea mays and the 3′ untranslatedregion (UTR) comprising the transcriptional terminator andpolyadenylation site of the nopaline synthase gene (nos) from A.tumefaciens pTi15955. The AHAS (P197S) coding sequence was amplifiedwith flanking attB sites and sub-cloned into pDONR221. The resultingENTRY clone was used in a LR CLONASE II® (Invitrogen, Life Technologies)reaction with the Gateway-enabled binary vector encoding thephosphinothricin acetyl transferase (PAT) expression cassette. Coloniesof all assembled plasmids were initially screened by restrictiondigestion of miniprep DNA. Restriction endonucleases were obtained fromNew England BioLabs (NEB; Ipswich, MA) and Promega (Promega Corporation,WI). Plasmid preparations were performed using the QIAPREP SPIN MINIPREPKIT® (Qiagen, Hilden) or the PURE YIELD PLASMID MAXIPREP SYSTEM®(Promega Corporation, WI) following the instructions of the suppliers.Plasmid DNA of selected clones was sequenced using ABI Sanger Sequencingand BIG DYE TERMINATOR V3.1® cycle sequencing protocol (AppliedBiosystems, Life Technologies). Sequence data were assembled andanalyzed using the SEQUENCHER™ software (Gene Codes Corporation, AnnArbor, Mich.).

The resulting binary expression clone pDAS000164 was transformed intoAgrobacterium tumefaciens strain EHA105. Transgenic wheat plants withrandomly integrated T-DNA were generated by Agrobacterium-mediatedtransformation using the donor wheat line cv. Bobwhite MPB26RH,following a protocol similar to Wu et al. (2008) Transgenic Research17:425-436. Putative T₀ transgenic events expressing the AHAS (P197)expression constructs were selected for phosphinothricin (PPT)tolerance, the phenotype conferred by the PAT transgenic selectablemarker, and transferred to soil. The T₀ plants were grown underglasshouse containment conditions and T₁ seed was produced.

Genomic DNA from each T₀ plant was extracted from leaf tissue, using theprotocols as previously described in Example 6, and tested for thepresence or absence of carryover Agrobacterium tumefaciens strain andfor the number of integrated copies of the T-DNA encoding AHAS (P197S).The presence or absence of the A. tumefaciens strain was performed usinga duplex hydrolysis probe qPCR assay (analogous to TAQMAN™) to amplifythe endogenous ubiquitin gene (SEQ ID NO:290, SEQ ID NO:291, and SEQ IDNO:292 for forward and reverse primers and probe sequence, respectively)from the wheat genome, and virC from pTiBo542 (SEQ ID NO: 293, SEQ IDNO:294, and SEQ ID NO:70 for forward and reverse primers and probesequence, respectively). The number of integrated T-DNA copies wasestimated using a duplex hydrolysis probe qPCR assay, as previouslydescribed in Example 6, based on the puroindoline-b gene (Pinb) from theD genome of hexaploid wheat and a region of the Actin (Act1) promoterpresent on pDAS000164. Overall, 35 independent T₀ events with fewer thanthree randomly integrated copies of T-DNA were generated.

Optimization of Chemical Selection Conditions; Conditions forRegenerating Wheat Plants on Sulfometuron Methyl

A series of experiments were performed to determine optimal selectionconditions for regenerating wheat plants expressing the AHAS (P197S)mutation conferring tolerance to sulfonylurea class herbicides. Theseexperiments were based on testing the basal tolerance of the wild-typedonor wheat line cv. Bobwhite MPB26RH (P197/P197 genotype, which conferssusceptibility to sulfonylureas) at the callus induction, plantregeneration and rooting stages of an established wheat transformationsystem. Similar experiments were performed to determine the basaltolerance of transgenic cv. Bobwhite MPB26RH events that had randomlyintegrated T-DNA expressing the AHAS (P197S) mutation, which conferstolerance to sulfonylurea selection agents.

The basal tolerance of the wild-type donor wheat line to sulfometuronmethyl at the callus induction stage was determined as follows: scutellaof immature zygotic embryos were isolated, as previously described inExample 4, and placed in 10 cm petri dishes containing CIM mediumsupplemented with 0, 100, 500, 1000, 1500 and 2000 nM sulfometuronmethyl, respectively. Twenty scutella were placed in each petri dish. Atotal of 60 scutella were tested at each sulfometuron methylconcentration. After incubation at 24° C. in the dark for 4 weeks, theamount of somatic embryogenic callus formation (SEC) at eachsulfometuron methyl concentration was recorded. The results showed thatSEC formation for cv. Bobwhite MPB26RH was reduced by about 70% at 100nM sulfometuron methyl, compared to untreated samples.

The basal tolerance of the wild-type donor wheat line to sulfometuronmethyl at the plant regeneration stage was determined as follows:scutella of immature zygotic embryos from the donor wheat line wereisolated and placed in 10 cm petri dishes containing CIM medium. ThenSEC was allowed to form by incubating at 24° C. in the dark for 4 weeks.The SEC was transferred to 10 cm petri dishes containing DRM mediumsupplemented with 0, 100, 500, 1000, 1500, 2000, 2500 and 3000 nMsulfometuron methyl, respectively. Twenty CIM were placed in each petridish. A total of 60 CIM were tested for basal tolerance response at eachsulfometuron methyl concentration. After incubation for 2 weeks at 24°C. under a 16/8 (light/dark) hour photoperiod in a growth room, theregeneration response was recorded. The results showed that plantregeneration was reduced by about 80% at 2000 nM sulfometuron methyl,compared to untreated samples.

The basal tolerance of the wild-type donor wheat line to sulfometuronmethyl at the plant rooting stage was determined as follows: scutella ofimmature zygotic embryos were isolated and placed in 10 cm petri dishescontaining CIM medium. Then SEC was allowed to form by incubating at 24°C. in the dark for 4 weeks. The SEC was transferred to 10 cm petridishes containing DRM medium and incubated for 2 weeks at 24° C. under a16/8 (light/dark) hour photoperiod to allow plant regeneration to takeplace. Regenerated plants were transferred to 10 cm petri dishescontaining RM medium supplemented with 0, 100, 200, 250, 300, 400, 500,1000 and 2000 nM sulfometuron methyl, respectively. Ten regeneratedplants were placed in each petri dish. A total of 30 regenerated plantswere tested for basal tolerance response at each sulfometuron methylconcentration. After incubation for 3 weeks at 24° C. under a 16/8(light/dark) hour photoperiod in a growth room, the root formationresponse was recorded. The results showed that root formation wasseverely inhibited when concentrations of sulfometuron methyl higherthan 400 nM, compared to untreated samples.

The basal tolerance of transgenic wheat events with randomly integrated,low-copy (≦3) T-DNA expressing the AHAS (P197S) mutation to sulfometuronmethyl from pDAS000164 at the plant rooting stage was determined asfollows: four independent transgenic events were randomly selected andmultiplied in vitro by sub-culturing on multiplication medium. Followingmultiplication, plants for each event were transferred to 10 cm petridishes containing RM medium supplemented with 0, 400, 450, 500, 550 and600 nM sulfometuron methyl, respectively. Four plants (one from each ofthe four events) were placed in each petri dish. A total of 3 plants perevent were tested for basal tolerance at each sulfometuron methylconcentration. After incubation for 2 weeks at 24° C. under a 16/8(light/dark) hour photoperiod in a growth room, the root formationresponse was recorded. The results showed that root formation was notrestricted, compared to untreated controls, at any of the concentrationstested, indicating that the AHAS (P197S) mutation conferred hightolerance to sulfometuron methyl.

Design and Synthesis of Donor DNA for First Sequential TransgeneStacking at an Endogenous AHAS Locus Using NHEJ-Directed DNA Repair

The donor DNA of the pDAS000433 construct (FIG. 12) for the first roundof transgene stacking is designed and synthesized as described inExamples 10 and 11 to promote precise donor integration (containing theS653N mutation) at an endogenous AHAS locus via ZFN-mediated,NHEJ-directed repair. Whole plants that are resistant to IMAZAMOX® areobtained and prepared for a second round of targeting to introduce the

Design and Synthesis of Donor DNA for Second Sequential Transgene Stackat an Endogenous AHAS Locus Using NHEJ-Directed DNA Repair

The donor DNA (pDAS000434; FIG. 13; SEQ ID NO:72) containing a P197Smutation for the second round of transgene stacking is designed topromote precise donor integration at the same AHAS locus targeted in thefirst transgene stack via ZFN-mediated, NHEJ-directed repair. The designis based on the integration of a double stranded donor molecule at thedouble strand DNA break created by cleavage of the AHAS gene copycontaining the first stacked transgene by ZFNs 34480 and 34481 (encodedon plasmid pDAB111860) or ZFNs 34482 and 34483 (encoded on plasmidpDAB111861). The pDAS000434 donor molecule comprises several portions ofpolynucleotide sequences. The 5′ end contains sequence nearly identicalto the endogenous AHAS gene encoded in the D-genome, starting from thetarget ZFN cleavage site and finishing at the AHAS stop codon. Severaldeliberate mutations are introduced into this sequence: mutationsencoding the P197S mutation and codon-optimized, synonymous mutationspositioned across the binding site of ZFNs 34481 and 34483 to preventre-cleavage of the integrated donor. Following the stop codon is 316-bpof non-coding sequence corresponding to the conserved 3′ untranslatedregion (3′UTR) in the AHAS homoeologs. The 3′UTR sequence is followed byZinc Finger binding sites for ZFNs 34474 and 34475 (encoded on plasmidpDAB111857) and ZFNs 34476 and 34477 (encoded on plasmid pDAB111858).These Zinc Finger binding sites allow for self-excision of donor-derivedAHAS (coding and 3′UTR) sequence integrated at an endogenous locus inthe next round of transgene stacking. The self-excision Zinc Fingerbinding sites are followed by several additional Zinc Finger bindingsites (each of which is separated by 100-bp of random sequence) thatflank unique restriction endonuclease cleavage sites, and which enableinsertion of a transgene expression cassette (e.g., the DGT-28expression cassette, as described in U.S. Pat. Pub. No. 20130205440).The additional Zinc Finger binding sites enable future excision oftransgenes that can be integrated at an AHAS locus by sequentialmarker-free transgene stacking, or continued sequential transgenestacking at the same genomic location using an alternate stackingmethod. The donor cassette is synthesized by a commercial gene servicevendor (e.g., GeneArt, Life Sciences) with a short stretch of additionalflanking sequence at the 5′ and 3′ ends to enable generation of a donormolecule with protruding 5′ and 3′ ends that are compatible with theligation overhangs generated by ZFNs 34474 and 34475 (encoded on plasmidpDAB111857) or ZFNs 34476 and 34477 (encoded on plasmid pDAB111858),upon cleavage of an endogenous AHAS locus.

The donor molecule with protruding 5′ and 3′ ends is generated bydigesting plasmid DNA containing the donor molecule, or following PCRamplification as described for “QA_pDAS000434” and/or pDAS000433, withthe restriction endonuclease BbsI using standard methods known to one inthe art.

Transformation System for Exogenous Marker-Free, Sequential TransgeneStacking at an Endogenous AHAS Locus in Wheat Using NHEJ-Directed DNARepair

Transgenic wheat events with multiple transgenes stacked at the sameendogenous AHAS locus are produced by exogenous marker-free, sequentialtransgene stacking via transformation with donor pDAS000433 and ZFNs29732 and 29730 (encoded on plasmid pDAB109350). Precise ZFN-mediated,NHEJ-directed donor integration introduces the first transgene and S653Nmutation conferring tolerance to imidazolinones at an AHAS locus, thusallowing for the regeneration of correctly targeted plants usingIMAZAMOX® as a selection agent, as previously described in Example 5.FIG. 14 a depicts the integration. Subsequent transformation of wheatcells, derived from first transgene stacked events, with donorpDAS000434 and ZFNs 34480 and 34481 (encoded on plasmid pDAB111860)results in the replacement of the endogenous chromatin located betweenthe ZFN binding sites positioned upstream of P197 and at theself-excision site integrated during the first transgene stack with thedonor molecule. This results in integration of the second transgene anda P197S mutation conferring tolerance to sulfonylurea, thus allowing forthe regeneration of correctly targeted plants using sulfometuron methylas a selection agent. At the same time, integration of the second donorremoves the S653N mutation, thus restoring susceptibility toimidazolinones (FIG. 14 b). One skilled in the art will appreciate thatstacking of a third transgene can be achieved by transformation withappropriate zinc finger nucleases and a donor that contains anadditional transgene and confers susceptibility to sulfonylurea andtolerance to imidazolinones, thus allowing the regeneration of correctlytargeted plants using IMAZAMOX® as a selection agent. As such, continuedrounds of sequential transgene stacking are possible via transformationwith donors that introduce transgenes and mutations in the endogenousAHAS genes for differential cycling between imidazolinone andsulfonylurea selection agents.

The transformation system used to regenerate wheat plants withsequentially stacked transgenes at an endogenous AHAS locus is based onthe previously described approach for biolistics-mediated DNA deliveryto scutella of immature zygotic wheat embryos, or direct DNA delivery towheat protoplasts using approaches known to one skilled in the art; forexample, using the method of He et al. (1994) Plant Cell Reports 14:92-196, or any of the methods described in Example 11.

Design and Synthesis of Donor DNA for First Sequential TransgeneStacking at an Endogenous AHAS Locus Using HDR-Directed DNA Repair

The donor DNA for the first round of transgene stacking is designed topromote precise donor integration at an endogenous AHAS locus viaZFN-mediated, HDR-directed homology repair. The design is based on theintegration of a double stranded donor molecule at the position of thedouble strand DNA break created by cleavage of a homoeologous copy ofthe endogenous AHAS gene by ZFNs 29732 and 29730 (encoded on plasmidpDAB109350). The donor molecule (pDAS000435; FIG. 16; SEQ ID NO:295) isidentical in sequence to pDAS000433 (FIG. 12).

The donor cassette is synthesized by a commercial gene service vendor(e.g., GeneArt, Life Sciences, etc.) with 750-bp homology arms at eachend. The homology arms at the 5′ and 3′ ends of the donor correspond toendogenous AHAS sequence immediately upstream and downstream of thedouble strand DNA break created by ZFNs 29732 and 29730 (encoded onplasmid pDAB109350).

Design and Synthesis of Donor DNA for Second Sequential TransgeneStacking at an Endogenous AHAS Locus Using HDR-Directed DNA Repair

The donor DNA for the second round of transgene stacking is designed topromote precise donor integration at the same AHAS locus targeted in thefirst transgene stack via ZFN-mediated, HDR-directed homology repair.The design is based on the integration of a double stranded donormolecule at the double strand DNA break created by cleavage of the AHASgene copy containing the first stacked transgene by ZFNs 34480 and 34481(encoded on plasmid pDAB111860) or ZFNs 34482 and 34483 (encoded onplasmid pDAB111861). The donor molecule (pDAS000436; FIG. 17; SEQ IDNO:296) is identical in sequence to pDAS000434 (FIG. 13).

The donor cassette is synthesized by a commercial gene service vendor(e.g., GeneArt, Life Sciences, etc.) with 750-bp homology arms at eachend. The homology arm at the 5′ end of the donor corresponds toendogenous AHAS sequence immediately upstream of the double strand DNAbreak created by ZFNs 34480 and 34481 (encoded on plasmid pDAB111860).The homology arm at the 3′ end of the donor corresponds to GOI-1sequence adjacent to the double stand DNA break created by ZFNs 34480and 34481 in the donor DNA integrated in the first transgene stack.

Transformation System for Exogenous Marker-Free, Sequential TransgeneStacking at an Endogenous AHAS Locus in Wheat Using HDR-Directed DNARepair

Transgenic wheat events with multiple transgenes stacked at the sameendogenous AHAS locus are produced by exogenous transgenic marker-free,sequential stacking of transgenes encoding traits (without use of atransgenic marker) via transformation with donor pDAS000435 and ZFNs29732 and 29730 (encoded on plasmid pDAB109350). Precise ZFN-mediated,HDR-directed donor integration introduces the first transgene and S653Nmutation conferring tolerance to imidazolinones at an AHAS locus, thusallowing for the regeneration of correctly targeted plants usingIMAZAMOX® as a selection agent, as previously described in Example 5.FIG. 15 a depicts the integration. Subsequent transformation of wheatcells, derived from first transgene stacked events, with donorpDAS000436 and ZFNs 34480 and 34481 (encoded on plasmid pDAB111860)results in the replacement of the endogenous chromatin located betweenthe ZFN binding sites positioned upstream of P197 and at theself-excision site integrated during the first transgene stack with thedonor molecule. This results in integration of the second transgene, anda P197S mutation conferring tolerance to sulfonylurea. Subsequently, theintegration of the second transgene allows for the regeneration ofcorrectly targeted plants using sulfometuron methyl as a selectionagent. At the same time, integration of the second donor removes theS653N mutation, thus restoring susceptibility to imidazolinones (FIG. 15b). As will be obvious to one skilled in the art, stacking of a thirdtransgene can be achieved by transformation with appropriate zinc fingernucleases and a donor that contains an additional transgene and conferssusceptibility to sulfonylurea and tolerance to imidazolines, thusallowing the regeneration of correctly targeted plants using IMAZAMOX®as a selection agent. As such, continued rounds of sequential transgenestacking are possible via transformation with donors that introducetransgenes and mutations in the endogenous AHAS genes for differentialcycling between imidazolinone and sulfonylurea selection agents.

The transformation system used to regenerate wheat plants withsequentially stacked transgenes at an endogenous AHAS locus is based onthe previously described approach for biolistics-mediated DNA deliveryto scutella of immature zygotic wheat embryos, or direct DNA delivery towheat protoplasts using approaches known to one skilled in the art; forexample, using the of He et al. (1994) Plant Cell Reports 14: 92-196, orany of the methods described in Example 11.

Example 13 Development of a Transformation System for ExogenousMarker-Free Genome Editing at a Non-Selectable Trait Locus in Wheat

Precision genome modification of endogenous loci provides an effectualapproach to modify trait expression. The generation of exogenousmarker-free transformation events with precise genome modifications atone or more non-selectable endogenous trait loci provides opportunitiesto create new and novel high-value alleles for crop improvement. Here,we describe the development of a transformation system for ZFN-mediated,exogenous marker-free, precision genome editing at non-selectable traitloci in wheat that can be adapted for both integrative andnon-integrative trait modification.

The transformation system is based on a two-step process. In the firststep, ZFN-mediated precision genome modification is used tosimultaneously modify two independent loci in the plant genome; onelocus is modified to confer tolerance to a selectable marker, the otheris modified to alter expression for a non-selectable trait of interest.Transformation T0 events co-edited at both loci are generated byselecting for the introduced exogenous selectable marker. In the secondstep, marker-free events with only the modified trait locus arerecovered by PCR screening of segregating T1 plants. The approach can beadapted for non-integrative precision genome modification that resultsin either the ablation of the non-selectable endogenous gene, orre-writing (editing) of the nucleotide sequence of the non-selectableendogenous gene. Alternatively, the approach can be adapted forintegrative precision genome modification in which the function of thenon-selectable endogenous gene is altered. More broadly, the approachcould be adapted for non-integrative precision genome modification inwhich previously integrated exogenous DNA, for example a transgene, isexcised.

The endogenous AHAS gene in wheat was selected as a model locus toestablish and validate the transformation system for exogenousmarker-free precision genome editing at a non-selectable trait locus inwheat.

Preparation of Donor DNA for ZFN-Mediated NHEJ-Directed AHAS GeneEditing

The donor DNA molecule, pDAS000267 (SEQ ID NO:84 and SEQ ID NO:85) wasdesigned and synthesized as described in Example 6. Briefly, the donorDNA consisted a 95-bp double stranded molecule that was designed tointegrate at the position of the double strand DNA break created bycleavage of a homoeologous copy of the endogenous AHAS gene by ZFNs29732 and 29730 (encoded on plasmid pDAB109350). The pDAS000267construct consisted of two parts. The 5′ end contained sequence nearlyidentical to the endogenous AHAS gene encoded in the D-genome, startingfrom the target ZFN cleavage site and finishing at the AHAS stop codon.Six intentional mutations were introduced into this sequence: twomutations encoded the S653N mutation (AGC→AAT), and four synonymousmutations (in which a silent mutation was incorporated into the donorsequence). The 3′ end of the donor molecule contained a unique sequencethat could be used for diagnostic PCR to detect ZFN-mediatedNHEJ-directed gene editing events. The donor molecule was designed withprotruding 5′ and 3′ ends to provide ligation overhangs to facilitateZFN-mediated NHEJ-directed DNA repair.

Preparation of ZFN Construct DNA

Plasmid DNA for pDAB109350 (FIG. 1) encoding ZFNs 29732 and 29730 wasprepared from cultures of E. coli using the PURE YIELD PLASMID MAXIPREPSYSTEM® (Promega Corporation, Madison, Wis.) following themanufacturer's instructions.

Design and Production of Binary Vector Encoding PAT Selection Cassette

Standard cloning methods were used to construct the binary vectorpDAS000004 (SEQ ID:303; FIG. 18). The PAT selection cassette consistedof the promoter, 5′ untranslated region and intron from the Actin (Act1)gene from Oryza sativa (McElroy et al., (1990) The Plant Cell 2(2):163-171) followed by a synthetic, plant-optimized version ofphosphinothricin acetyl transferase (PAT) gene, isolated fromStreptomyces viridochromogenes, which encodes a protein that confersresistance to inhibitors of glutamine synthetase comprisingphosphinothricin, glufosinate, and bialaphos (Wohlleben et al., (1988)Gene, 70(1): 25-37). This cassette was terminated with the 3′ UTRcomprising the transcriptional terminator and polyadenylation sites fromthe 35s gene of cauliflower mosaic virus (CaMV) (Chenault et al., (1993)Plant Physiology 101 (4): 1395-1396).

The selection cassette was synthesized by a commercial gene synthesisvendor (GeneArt, Life Technologies, etc.) and cloned intoGateway-enabled binary vector. Colonies of the assembled plasmid werescreened by restriction digestion of miniprep DNA using restrictionendonucleases obtained from New England BioLabs and Promega. Plasmidpreparations were performed using the QIAPREP SPIN MINIPREP KIT™following the manufacturer's instructions. Plasmid DNA of selectedclones was sequenced using ABI Sanger Sequencing and BIG DYE TERMINATORv3.1™ cycle sequencing protocol (Applied Biosystems, Life Technologies).Sequence data were assembled and analyzed using the SEQUENCHER™ software(Gene Codes Corporation, Ann Arbor, Mich.). Plasmid DNA used fortransfection was prepared from cultures of E. coli using the PURE YIELDPLASMID MAXIPREP SYSTEM® (Promega Corporation, Madison, Wis.) followingthe manufacturer's instructions.

Biolistic-Mediated Transformation System for Generating ExogenousMarker-Free Wheat Plants with Precise Genome Modifications atNon-Selectable Endogenous Trait Loci

A total of 2,320 scutella of immature zygotic embryos from the donorwheat line cv. Bobwhite MPB26RH were prepared for biolistics-mediatedDNA delivery, as described previously. DNA-coated gold particles wereprepared as described above using a DNA mixture comprising 2.5 μg ofdonor pDAS000267 and plasmid pDAB109350 (at a molar ratio of 7:1,respectively) and 2.5 μg of plasmid pDAS000004.

Following bombardment, the transfected scutella were incubated at 26° C.in the dark for 16 h before being transferred onto medium for callusinduction. The scutella were cultured in the dark on callus inductionmedium at 24° C. for 2 weeks. The resultant calli were sub-cultured onceonto fresh callus induction medium, and kept in the same conditions fora further two weeks. The SEC was transferred onto plant regenerationmedium containing 5 mg/ml BASTA® and cultured for 2 weeks at 24° C.under a 16/8 (light/dark) hour photoperiod in a growth room. Regeneratedplantlets were transferred onto rooting medium containing 5 mg/ml BASTA®and cultured under the same conditions for 2-3 weeks. Regeneratedplantlets producing roots were expected have one or more copies of thePAT selection cassette randomly inserted into the plant genome. Theroots of these plantlets were removed and the plants were againsub-cultured on rooting media containing 200 nM IMAZAMOX® under the sameconditions for 2-3 weeks. Plants with regrown roots were expected tohave the S653N mutation (resulting from precise integration ofpDAS000267) in one or more copies of endogenous AHAS gene.

A total of 170 wheat plants producing strong root growth on rootingmedium containing BASTA® were obtained from the transfection of the2,320 scutella of immature zygotic embryos from the donor wheat line cv.Bobwhite MPB26RH. Of these, two wheat plants produced roots whentransferred to rooting medium containing IMAZAMOX®. These plants weretransferred to soil and grown under glasshouse containment conditions toproduce T1 seed.

Optimization of BASTA® Chemical Selection for Enrichment of TransformedEvents in a Wheat Protoplast-Based Transformation System

A series of experiments are performed to determine optimal selectionconditions for regenerating wheat plants expressing the PAT geneconferring tolerance to BASTA® from a protoplast-based transformationsystem such as those described by Qiao et al. (1992) Plant Cell Reports11:262-265; Ahmed and Sagi (1993) Plant Cell Reports 12:175-179; Pauk etal. (1994) Plant Cell, Tissue and Organ Culture 38: 1-10; He et al.(1994) Plant Cell Reports 14: 92-196; Gu and Lang (1997) Plant Cell,Tissue and Organ Culture 50: 139-145; and Li et al. (1999) Plant Cell,Tissue and Organ Culture 58: 119-125.

BASTA® selection conditions are optimized using protoplasts derived fromsomatic embryogenic callus (SEC)-derived cell suspension culture of thewheat line cv. Bobwhite MPB26RH. While protoplasts derived from BobwhiteMPB26RH are non-totipotent (i.e., cannot be used to regenerate entireplants), the selection conditions established for enriching the eventsthat express the PAT gene are expected to be transferable to anyprotoplast-based transformation system based on a totipotent wheatgenotype. The experiments are conducted, and the basal tolerance of thewild-type donor wheat line cv. Bobwhite MPB26RH to BASTA® isestablished. The use of BASTA® selection conditions stronger than basaltolerance are identified and used to select for transformed cellsexpressing the PAT gene.

Establishment of Agarose Bead-Type Cultures and BASTA® SelectionConditions

Protoplasts are isolated from an established SEC-derived cell suspensionculture and used to establish agarose bead-types cultures, as describedpreviously. The basal tolerance of wheat line cv. Bobwhite MPB26RH toBASTA® is determined by incubating the agarose bead-type cultures inmedia supplemented with 0, 0.5, 2.5, 5, 7.5, 10, 20, 30, 40 and 50 mg/LBASTA® and assessing the rate of calli growth after 2 weeks. The BASTA®concentrations (e.g., higher than 20 mg/L) that severely impeded callidevelopment are optimal for enriching and selecting wheat cells havingthe PAT gene.

Molecular Characterization of the Transformed Wheat Plants with BASTA®and IMAZAMOX® Tolerant Phenotypes

The two wheat plants having both the BASTA® and IMAZAMOX® herbicidetolerant phenotypes were molecularly characterized to identify theendogenous AHAS gene that contained the S653N mutation resulting fromintegration of pDAS000267 donor at a genomic double cleavage sitecreated by ZFNs 29732 and 29730 encoded on pDAB109350.

Two molecular assays were performed for each wheat plant using genomicDNA extracted with the DNEASY® PLANT DNA EXTRACTION MINI KIT™ (Qiagen)from freeze-dried leaf tissue, as described previously.

The first molecular test was used to confirm that the regenerated wheatplants had at least one randomly integrated copy of the PAT gene. Aduplex hydrolysis probe qPCR assay (analogous to TAQMAN®) was used toamplify the endogenous single copy gene, puroindoline-b (Pinb) gene,from the D genome of hexaploid wheat (Gautier et al., (2000) PlantScience 153, 81-91; SEQ ID NO: 89, SEQ ID NO: 90 and SEQ ID NO: 91 forforward primer, reverse primer, and probe sequence, respectively) and aregion of the Actin (Act1) promoter present on pDAS000004 (SEQ ID NO:92, SEQ ID NO: 93 and SEQ ID NO: 94 for forward primer, reverse primer,and probe sequence, respectively). Assessment for the presence, andestimated copy number of pDAS000004 was performed according to themethod described in Livak and Schmittgen (2001) Methods 25(4):402-8.From the results, evidence was obtained for the integration of the PATpolynucleotide sequence into the genome of wheat plant eventsyc06-9110-1 and yr00-9311-1, respectively.

The second molecular test was used to characterize the sub-genomiclocation and outcome for ZFN-mediated NHEJ-directed donor integration atthe endogenous AHAS genes. PCR with primers AHASs653ZFN.F2 andAHASs653ZFN.R1 (SEQ ID NO: 301 and 302; Table 18) was used to amplifythe DNA fragment from each of the three homoeologous copies of theendogenous AHAS gene. The amplified fragment contained a regioncontaining the binding site for ZFNs 29732 and 29730 (encoded on plasmidpDAB190350), and to include genomic nucleotide sequence variation.Enough genomic nucleotide sequence variation was included todifferentiate between the AHAS homoeologs, such that the resultingamplicons could be unequivocally attributed (at the sequence level) tothe wheat sub-genome from which they were derived. The resultingamplicons were prepared for deep sequencing as described in Example 12and sequenced on an Illumina MiSEQ™ instrument to generate 250-bppaired-end sequence reads, according to the manufacturer's instructions.The resultant sequence reads were computationally processed, asdescribed previously, to assign each read to sample (based on thebarcode index) and the sub-genome from which they were derived (based onnucleotide variation that distinguished between homoeologous copies ofthe AHAS gene). As described in Example 9, the integration of pDAS000267into an endogenous AHAS locus results in a 95-bp size difference betweenthe wild-type (unmodified) and resulting transgenic (modified) allele.Hence, PCR amplification of both the wild-type and modified AHAS geneloci is expected. Custom developed PERL scripts and manual datamanipulation in MICROSOFT EXCEL 2010™ (Microsoft Corporation) were usedto characterize the sub-genomic location and outcome for donorintegration into the endogenous AHAS genes.

From the results of the second molecular assay, conclusive evidence forprecise ZFN-mediated NHEJ-directed gene editing at an endogenous AHASlocus was demonstrated for both wheat plants. Event yc06-9110-1 hadperfect hemizygous donor integration in the B-genome (Table 24). Eventyr00-9311-1 had simultaneous donor integration into multiplesub-genomes. In the A-genome, independent editing of both endogenousAHAS loci was observed. One allele had partial donor integration thatresulted in the expected integration of the S653N mutation forexpression of the AHAS herbicide tolerance phenotype. However, afragment spanning 24-bp nucleotides were deleted from the 3′ end of thedonor molecule. The other allele had integration of a 51-bppolynucleotide sequence of unknown origin. No sequence reads originatingfrom the B-genome were obtained, suggesting independent integration of alarge polynucleotide sequence into each of the endogenous AHAS loci(Table 24). Consensus sequences for the alleles present in eachsub-genome for two regenerated wheat plants are provided as SEQ ID NOs:304-313. The absence of evidence of sequence originating frompDAS0000004 in both wheat plant events indicates that the PAT geneconferring tolerance to BASTA® was randomly integrated into a differentlocus in the plant genome.

TABLE 24 ZFN-mediated NHEJ-directed AHAS editing outcomes for wheatplants yc06-9110-1 and yr00-9311-1 A-genome B-genome D-genome Allele 1Allele 2 Allele 1 Allele 2 Allele 1 Allele 2 SEQ ID NO: yc06- Status UEUE PE UE UE UE 304-309 9110-1 No. 143,159 76,903 110,846 219,858 Reads¹yr00- Status IE IE nd nd UE UE 310-313 9311-1 No. 164,038 138,539 0556,123 Reads¹ ¹Number of sequence reads originating from the specifiedsub-genome and having the sequence haplotype corresponding to wild-type(unmodified) or transgenic (modified) AHAS loci. “PE” indicates perfectedit; i.e., ZFN-mediated NHEJ-directed genome editing produced apredicted outcome. “IE” indicates imperfect edit; i.e., ZFN-mediatedNHEJ-directed genome editing produced an unpredicted outcome. “UE”indicates unedited allele; i.e., allele had wild-type sequence. “nd”indicates not detected.

These results disclose for the first time a transformation method whichcan be utilized to generate exogenous marker-free wheat plants havingprecise genome modifications at one or more non-selectable trait loci.Wheat plants comprising an integrated AHAS donor polynucleotide encodinga S653N mutation conferring tolerance to imidazolinone class herbicidesare exemplified. As will be appreciated by one skilled in the art, wheatplants without the exogenous transgenic selectable marker (e.g., PAT)can be recovered by screening T1 plants derived from these events usingPCR assays specific for either the PAT or the modified AHAS genes.

All patents, patent applications and publications mentioned herein arehereby incorporated by reference in their entirety.

Although disclosure has been provided in some detail by way ofillustration and example for the purposes of clarity of understanding,it will be apparent to those skilled in the art that various changes andmodifications can be practiced without departing from the spirit orscope of the disclosure. Accordingly, the foregoing descriptions andexamples should not be construed as limiting.

What is claimed is:
 1. A plant cell comprising a targeted genomicmodification to one or more alleles of an endogenous gene in the plantcell, wherein the genomic modification follows cleavage by a sitespecific nuclease, and wherein the genomic modification produces amutation in the endogenous gene such that the endogenous gene produces aproduct that results in an herbicide tolerant plant cell.
 2. The plantcell of claim 1, wherein the genomic modification comprises integrationof one or more exogenous sequences.
 3. The plant cell of claim 1,wherein the genomic modification comprises introduction of one or moreindels that disrupt expression of the endogenous gene.
 4. The plant cellof claim 1, wherein the endogenous gene with the genomic modificationencodes a protein that confers tolerance to sulfonylurea herbicides. 5.The plant cell of claim 1, wherein the endogenous gene with the genomicmodification encodes a protein that confers tolerance to imidazolinoneherbicides.
 6. The plant cell of claim 2, wherein the exogenous sequencedoes not encode a transgenic selectable marker.
 7. The plant cell ofclaim 2, wherein the exogenous sequence encodes a protein selected fromthe group consisting of a protein that increases crop yield, a proteinencoding disease resistance, a protein that increases growth, a proteinencoding insect resistance, a protein encoding herbicide tolerance, andcombinations thereof.
 8. The plant cell of claim 7, wherein theincreased crop yield comprises an increase in fruit yield, grain yield,biomass, fruit flesh content, size, dry weight, solids content, weight,color intensity, color uniformity, altered chemical characteristics, orcombinations thereof.
 9. The plant cell of claim 1, wherein theendogenous gene is an endogenous acetohydroxyacid synthase (AHAS) gene.10. The plant cell of claim 2, wherein two or more exogenous sequencesare integrated into the endogenous gene.
 11. The plant cell of claim 1,wherein the plant cell is a polyploid plant cell.
 12. The plant cell ofclaim 1, wherein the site specific nuclease comprises a zinc fingerDNA-binding domain, and a FokI cleavage domain.
 13. The plant cell ofclaim 12, wherein the zinc finger DNA-binding domain encodes a proteinthat binds to a target site selected from the group consisting of SEQ IDNOs:35-56 and 263-278.
 14. The plant cell of claim 1, wherein the plantis selected from the group consisting of wheat, soy, maize, potato,alfalfa, rice, barley, sunflower, tomato, Arabidopsis, cotton, Brassicaspecies, and timothy grass.
 15. A plant, plant part, seed, or fruitcomprising one or more plant cells of claim
 1. 16. The plant cell ofclaim 1, further comprising one or more transgenes integrated into thegenome of the plant cell at one or more loci different from theendogenous gene.
 17. A method for making a plant cell according to claim1, the method comprising: expressing one or more site specific nucleasesin the plant cell; and modifying one or more alleles of an endogenousgene across multiple genomes of a polyploid plant cell.
 18. The methodof claim 17, wherein the endogenous gene is an acetohydroxyacid synthase(AHAS) gene.
 19. The method of claim 17, wherein the modificationdisrupts expression of the endogenous gene.
 20. The method of claim 17,wherein the modification comprises integration of one or more exogenoussequences into one or more alleles of the endogenous gene.
 21. A plant,plant part, seed, or fruit comprising one or more plant cells producedby the method of claim
 17. 22. A zinc finger protein that binds to atarget site selected from the group consisting of SEQ ID NOs:35-56 and263-278.
 23. The zinc finger protein of claim 22, comprising therecognition helix regions shown in a single row of Table 2 or Table 12.24. A method of integrating one or more exogenous sequences into thegenome of a plant cell, the method comprising: a) expressing one or moresite specific nucleases in the plant cell, wherein the one or morenucleases target and cleave chromosomal DNA of one or more endogenousloci; b) integrating one or more exogenous sequences into the one ormore endogenous loci within the genome of the plant cell, wherein theone or more endogenous loci are modified such that the endogenous geneis mutated to express a product that results in a selectable phenotypein the plant cell; and c) selecting plant cells that express theselectable phenotype, wherein plant cells are selected which incorporatethe one or more exogenous sequences.
 25. The method of claim 24, whereinthe one or more exogenous sequences are selected from the groupconsisting of a donor polynucleotide, a transgene, or any combinationthereof.
 26. The method of claim 24, wherein integrating the one or moreexogenous sequences occurs by homologous recombination or non-homologousend joining.
 27. The method of claim 24, wherein the one or moreexogenous sequences are incorporated simultaneously or sequentially intothe one or more endogenous loci.
 28. The method of claim 24, wherein theone or more endogenous loci comprise an acetohydroxyacid synthase (AHAS)gene.
 29. The method of claim 28, wherein the AHAS gene is located on anA, B, or D genome of a polyploidy genome.
 30. The method of claim 28,wherein the one or more exogenous sequences are integrated into the AHASgene.
 31. The method of claim 30, wherein the one or more exogenoussequences encode a S653N AHAS mutation.
 32. The method of claim 30,wherein the one or more exogenous sequences encode a P197S AHASmutation.
 33. The method of any of claim 24, wherein the site specificnuclease is selected from the group consisting of a zinc fingernuclease, a TAL effector domain nuclease, a homing endonuclease, and aCrispr/Cas single guide RNA nuclease.
 34. The method of claim 33,wherein the site specific nuclease comprises a zinc finger DNA-bindingdomain and a FokI cleavage domain.
 35. The method of any claim 24,wherein the one or more exogenous sequences encode a transgene orproduce an RNA molecule.
 36. The method of claim 35, wherein thetransgene encodes a protein selected from the group consisting of aprotein that increases crop yield, a protein encoding diseaseresistance, a protein that increases growth, a protein encoding insectresistance, a protein encoding herbicide tolerance, and combinationsthereof.
 37. The method of claim 35, wherein the integration of thetransgene further comprises introduction of one or more indels thatdisrupt expression of the one or more endogenous loci and produce theselectable phenotype.
 38. The method of claim 24, the method furthercomprising the steps of; d) culturing the selected plant cellscomprising the one or more exogenous sequences; and e) obtaining a wholeplant comprising the one or more exogenous sequences integrated withinthe one or more endogenous loci of the plant genome.
 39. The method ofclaim 24, wherein a selection agent comprising an imidazolinone, or asulfonylurea selection agent is used to select the plant cells.
 40. Themethod of claim 38, wherein the whole plant comprising the one or moreexogenous sequences integrated within the one or more endogenous loci ofthe plant genome is further modified to incorporate an additionalexogenous sequence within the endogenous loci of the plant genome. 41.The method of claim 38, wherein the one or more exogenous sequence doesnot encode a transgenic selectable marker.